RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

Human genetic basis of coronavirus disease 2019

Coronavirus disease 2019 (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in considerable morbidity and mortality worldwide. COVID-19 incidence, severity, and mortality rates differ greatly between populations, genders, ABO blood groups, human leukocyte antigen (HLA) genotypes, ethnic groups, and geographic backgrounds. This highly heterogeneous SARS-CoV-2 infection is multifactorial. Host genetic factors such as variants in the angiotensin-converting enzyme gene (ACE), the angiotensin-converting enzyme 2 gene (ACE2), the transmembrane protease serine 2 gene (TMPRSS2), along with HLA genotype, and ABO blood group help to explain individual susceptibility, severity, and outcomes of COVID-19. This review is focused on COVID-19 clinical and viral characteristics, pathogenesis, and genetic findings, with particular attention on genetic diversity and variants. The human genetic basis could provide scientific bases for disease prediction and targeted therapy to address the COVID-19 scourge.

The origins of SARS-CoV-2: A critical review

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

Effect of COVID-19 on mental health among the young population in Lebanon

Background

COVID-19 is a global pandemic that has raised worldwide public health concerns. The wide spread of the virus has led to unprecedented disturbance to regular life for people around the globe and impacted their mental health.

Aims

The aims of the current study were to investigate the prevalence of psychiatric symptoms related to insomnia, depression, and anxiety, and identify risk factors contributing to psychological stress in Lebanese young population during COVID-19 pandemic.

Method

A cross-sectional study was done on the Lebanese young population. Participants were 4397 males and females aged 18 to 35 years who filled a self-administered online questionnaire. Three validated scales were used to measure the mental health status of the participants during the COVID-19 pandemic: 7-item Insomnia Severity Index for insomnia, the Patient Health Questionnaire 9-item depression module for depression, and the 7-item Generalized Anxiety Disorder scale for anxiety.

Results

The median interquartile range scores for anxiety, insomnia, and depression, were 8 (4–13), 10 (5–14), and 9 (5–12) respectively. Higher anxiety scores were reported with female gender (P < 0.001) and alcohol usage (P = 0.04). Moderate to severe insomnia was associated with single (P = 0.02) and divorced marital status (P = 0.003), university education (P < 0.001), consumption of caffeinated beverages (P = 0.02) and energy drinks (P = 0.03). Higher depression scores were associated with status of being the only person working at home (P = 0.01), family income more than 500 USD (P = 0.008), multiple insurance plans (P = 0.01), and contact with a confirmed COVID-19 case (P = 0.01).

Conclusions

The findings of this study demonstrate the considerable impact of COVID-19 pandemic and lockdown on Lebanese young population's mental status such as anxiety, depression and insomnia. Further follow-up studies are warranted to assess the long-term mental effects that can be imposed by the pandemic.

Longitudinal Characterization of Cytokine Overproduction: A Case Report in Critically Ill COVID-19 Patients With Hyperinflammation in Bronchoalveolar Lavage

Objectives: The longitudinal characterization and risk of poor outcomes related to cytokine overproduction in critical coronavirus disease 2019 (COVID-19) patients with hyperinflammation in bronchoalveolar lavage requires further investigation. Methods: We enrolled two critically ill patients with comorbidities diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detected by RT-PCR during hospitalization. Clinical characteristics, longitudinal immunological, and biochemical parameters of each critical COVID-19 case were collected. Main Results: The clinical characteristics and laboratory results of each case demonstrated critical symptoms of COVID-19 with poor outcomes. Both nasopharyngeal swabs and bronchoalveolar lavage fluid (BALF) samples tested positive for SARS-CoV-2. Two patients received targeted treatments against pathogen infection and inflammation in addition to interventional therapies, except for Patient 2, who received an additional artificial liver system treatment. Hyperinflammation with a dominantly high level of IL-6 was observed in BALF samples from both critical cases with decreased T cell populations. High levels of cytokines and pathological parameters were successively maintained in Patient 1, but rapidly reduced at the late treatment stage in Patient 2. The outcome of Patient 1 is death, whereas the outcome of Patient 2 is recovery. Conclusions: This case report suggests that a high risk of poor outcomes was related to a heavily hyperinflammatory milieu in both the blood and lungs of critical COVID-19 patients. The artificial liver intervention on cytokines overproduction might be beneficial for the recovery of critical COVID-19 patients as a reliable therapy that can be coordinated with targeted treatments, which ought to be further tested in adequately designed and powered clinical trials.

Age-stratified transmission model of COVID-19 in Ontario with human mobility during pandemic's first wave

In this work, we employ a data-fitted compartmental model to visualize the progression and behavioral response to COVID-19 that match provincial case data in Ontario, Canada from February to June of 2020. This is a "rear-view mirror" glance at how this region has responded to the 1st wave of the pandemic, when testing was sparse and NPI measures were the only remedy to stave off the pandemic. We use an SEIR-type model with age-stratified subpopulations and their corresponding contact rates and asymptomatic rates in order to incorporate heterogeneity in our population and to calibrate the time-dependent reduction of Ontario-specific contact rates to reflect intervention measures in the province throughout lockdown and various stages of social-distancing measures. Cellphone mobility data taken from Google, combining several mobility categories, allows us to investigate the effects of mobility reduction and other NPI measures on the evolution of the pandemic. Of interest here is our quantification of the effectiveness of Ontario's response to COVID-19 before and after provincial measures and our conclusion that the sharp decrease in mobility has had a pronounced effect in the first few weeks of the lockdown, while its effect is harder to infer once other NPI measures took hold.

Exploring the relationship between the COVID-19 pandemic and changes in travel behaviour: A qualitative study

During the COVID-19 crisis, a series of measures were taken to restrict travel and social activities outside the home in order to curb the pandemic and ameliorate its negative effects. These unprecedented measures have had a profound impact on the number and purposes of trips and modes of travel. In China, although the pandemic is now generally under control and transport availability has returned to nearly normal, the extent of the changes in travel behaviour wrought during and after the pandemic still remains unclear. Therefore, the aim of this paper is to investigate the differences in individual travel behaviours during and after the COVID-19 pandemic, using Huzhou as an example. Semi-structured interviews were used to examine the influence of COVID-19 on the travel behaviour and perceptions of different groups. The results indicate that, initially, travel demand was greatly reduced. Second, decreased travel reduced participation in activities, which can have adverse effects on people's health as well as their subjective well-being. Third, the degree and duration of such impacts varied from person to person. Students, lower income cohorts, groups living in small communities with insufficient green spaces, and those working in tourism, catering, informal businesses and transport-related sectors were more vulnerable than others. Policymakers, urban and transport planners should therefore pay attention to the social inequities that arise from unequal access to transport and heterogeneity between individuals. Additionally, public transport systems require further development to promote social cohesion.

Trend and prediction of COVID-19 outbreak in Iran: SEIR and ANFIS model

Background: Mathematical and predictive modeling approaches can be used in COVID-19 crisis to forecast the trend of new cases for healthcare management purposes. Given the COVID-19 disease pandemic, the prediction of the epidemic trend of this disease is so important.

Methods: We constructed an SEIR (Susceptible-Exposed-Infected-Recovered) model on the COVID-19 outbreak in Iran. We estimated model parameters by the data on notified cases in Iran in the time window 1/22/2020 – 20/7/2021. Global sensitivity analysis is performed to determine the correlation between epidemiological variables and SEIR model parameters and to assess SEIR model robustness against perturbation to parameters. We Combined Adaptive Neuro-Fuzzy Inference System (ANFIS) as a rigorous time series prediction approach with the SEIR model to predict the trend of COVID-19 new cases under two different scenarios including social distance and non-social distance.

Results: The SEIR and ANFIS model predicted new cases of COVID-19 for the period February 7, 2021, till August 7, 2021. Model predictions in the non-social distancing scenario indicate that the corona epidemic in Iran may recur as an immortal oscillation and Iran may undergo a recurrence of the third peak.

Conclusion: Combining parametrized SEIR model and ANFIS is effective in predicting the trend of COVID-19 new cases in Iran.

Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice

Coronaviruses (CoVs) can infect a variety of hosts, including humans, livestock and companion animals, and pose a serious threat to human health and the economy. The current COVID-19 pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed millions of people. Unfortunately, effective treatments for CoVs infection are still lacking, suggesting the importance of coronavirus vaccines. Our previous work showed that CoV nonstuctural protein 14 (nsp14) functions as (guanine-N7)-methyltransferase (N7-MTase), which is involved in RNA cap formation. Moreover, we found that N7-MTase is well conserved among different CoVs and is a universal target for developing antivirals against CoVs. Here, we show that N7-MTase of CoVs can be an ideal target for designing live attenuated vaccines. Using murine hepatitis virus strain A59 (MHV-A59), a representative and well-studied model of coronaviruses, we constructed N7-MTase-deficient recombinant MHV D330A and Y414A. These two mutants are highly attenuated in mice and exhibit similar replication efficiency to the wild-type (WT) virus in the cell culture. Furthermore, a single dose immunization of D330A or Y414A can induce long-term humoral immune responses and robust CD4⁺ and CD8⁺ T cell responses, which can provide full protection against the challenge of a lethal-dose of MHV-A59. Collectively, this study provides an ideal strategy to design live attenuated vaccines for coronavirus by abolishing viral RNA N7-MTase activity. This approach may apply to other RNA viruses that encode their own conservative viral N7-methyltransferase.

Numerical investigation on the transmission and dispersion of aerosols in a 7-stories building drainage system

In previous reports, the positive SARS-CoV-2 nucleic acid was detected in the fecal samples from confirmed pneumonia patients, suggesting a high probability of the fecal-oral transmission. To date, however, the role played by the drainage system of a high-rise building in the virus transmission is not clear and especially studies on the dynamics mechanism behind is scarce. From this point of view, the present work carries out a computational fluid dynamics (CFD) modeling to investigate the effects of the water seal effectiveness of the floor drain, the negative/positive pressures (P ₁ , P ₂ ) in the bathroom, temperature differential (ΔT), outside wind velocity (v), the piping fittings and the negative pressure at the cowl (P ₃ ) on the transmission of the virus-laden aerosol particles in a drainage system of a typical 7-storeys residential building. The CFD models are first validated by the previous experiments in literature. Numerical results imply that the drainage system might play an essential role to the virus transmission. Then, results indicate that, the leakage risk of the aerosol particles via the floor drain with inefficient water-seal (UFD) mainly exists at the upper floors above the neutral pressure level (NPL). Besides, the negative and positive pressures at the bathroom can enhance and reduce the exposure risk of aerosol particles from the corresponding UFD, respectively. The ΔT increasing does not modify the location of the NPL. Moreover, the exposure risk of aerosol particles can be effectively avoided by the well water-sealed floor drains and/or the presence of a proper negative pressure at the cowl on the top floor. Finally, based on the CFD results, several protection suggestions on the drainage system and human activities are provided.

Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection

BACKGROUND

During the current SARS-CoV-2 pandemic, the identification of effective antiviral drugs is crucial. Unfortunately, no specific treatment or vaccine is available to date.

OBJECTIVE

Here, we aimed to predict the interactions between SARS-CoV-2 proteins and protein targets from the human body for some flavone molecules (kaempferol, morin, pectolinarin, myricitrin, and herbacetin) in comparison to synthetic compounds (hydroxychloroquine, remdesivir, ribavirin, ritonavir, AMD-070, favipiravir).

METHODS

Using MOE software and advanced bioinformatics and cheminformatics portals, we conducted an extensive analysis based on various structural and functional features of compounds, such as their amphiphilic field, flexibility, and steric features. The structural similarity analysis of natural and synthetic compounds was performed using Tanimoto coefficients. The interactions of some compounds with SARS-CoV-2 3CLprotease or RNA-dependent RNA polymerase were described using 2D protein-ligand interaction diagrams based on known crystal structures. The potential targets of considered compounds were identified using the SwissTargetPrediction web tool.

RESULTS

Our results showed that remdesivir, pectolinarin, and ritonavir present a strong structural similarity which may be correlated to their similar biological activity. As common molecular targets of compounds in the human body, ritonavir, kaempferol, morin, and herbacetin can activate multidrug resistance-associated proteins, while remdesivir, ribavirin, and pectolinarin appear as ligands for adenosine receptors.

CONCLUSION

Our evaluation recommends remdesivir, pectolinarin, and ritonavir as promising anti-SARS-CoV-2 agents.

Various theranostics and immunization strategies based on nanotechnology against Covid-19 pandemic: An interdisciplinary view

COVID-19 pandemic is still a major risk to human civilization. Besides the global immunization policy, more than five lac new cases are documented everyday. Some countries newly implement partial/complete nationwid lockdown to mitigate recurrent community spreading. To avoid the new modified stain of SARS-CoV-2 spreading, some countries imposed any restriction on the movement of the citizens within or outside the country. Effective economical point of care diagnostic and therapeutic strategy is vigorously required to mitigate viral spread. Besides struggling with repurposed medicines, new engineered materials with multiple unique efficacies and specific antiviral potency against SARS-CoV-2 infection may be fruitful to save more lives. Nanotechnology-based engineering strategy sophisticated medicine with specific, effective and nonhazardous delivery mechanism for available repurposed antivirals as well as remedial for associated diseases due to malfeasance in immuno-system e.g. hypercytokinaemia, acute respiratory distress syndrome. This review will talk about gloomy but critical areas for nanoscientists to intervene and will showcase about the different laboratory diagnostic, prognostic strategies and their mode of actions. In addition, we speak about SARS-CoV-2 pathophysiology, pathogenicity and host specific interation with special emphasis on altered immuno-system and also perceptualized, copious ways to design prophylactic nanomedicines and next-generation vaccines based on recent findings.

Clinical laboratory evaluation of COVID-19

COVID-19, caused by SARS-CoV-2, is a highly infectious disease, and clinical laboratory detection has played important roles in its diagnosis and in evaluating progression of the disease. Nucleic acid amplification testing or gene sequencing can serve as pathogenic evidence of COVID-19 diagnosing for clinically suspected cases, and dynamic monitoring of specific antibodies (IgM, IgA, and IgG) is an effective complement for false-negative detection of SARS-CoV-2 nucleic acid. Antigen tests to identify SARS-CoV-2 are recommended in the first week of infection, which is associated with high viral loads. Additionally, many clinical laboratory indicators are abnormal as the disease evolves. For example, from moderate to severe and critical cases, leukocytes, neutrophils, and the neutrophil-lymphocyte ratio increase; conversely, lymphocytes decrease progressively but are over activated. LDH, AST, ALT, CK, high-sensitivity troponin I, and urea also increase progressively, and increased D-dimer is an indicator of severe disease and an independent risk factor for death. Severe infection leads to aggravation of inflammation. Inflammatory biomarkers and cytokines, such as CRP, SAA, ferritin, IL-6, and TNF-α, increase gradually. High-risk COVID-19 patients with severe disease, such as the elderly and those with underlying diseases (cardiovascular disease, diabetes, chronic respiratory disease, hypertension, obesity, and cancer), should be monitored dynamically, which will be helpful as an early warning of serious diseases.

RBM15-mediated N6-methyladenosine modification affects COVID-19 severity by regulating the expression of multitarget genes

Severe coronavirus disease 2019 (COVID-19) is characterized by symptoms of lymphopenia and multiorgan damage, but the underlying mechanisms remain unclear. To explore the function of N6-methyladenosine (m6A) modifications in COVID-19, we performed microarray analyses to comprehensively characterize the m6A epitranscriptome. The results revealed distinct global m6A profiles in severe and mild COVID-19 patients. Programmed cell death and inflammatory response were the major biological processes modulated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Further, RBM15, a major m6A methyltransferase, was significantly elevated and positively correlated with disease severity. Silencing RBM15 drastically reduced lymphocyte death in vitro. Knockdown of RBM15 remarkably suppressed the expression levels of multitarget genes related to programmed cell death and inflammatory response. This study shows that SARS-CoV-2 infection alters the m6A epitranscriptome of lymphocytes, particularly in the case of severe patients. RBM15 regulated host immune response to SARS-CoV-2 by elevating m6A modifications of multitarget genes. These findings indicate that RBM15 can serve as a target for the treatment of COVID-19.

Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations

The ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a severe threat to human health and the global economy and has resulted in overwhelming stress on health care systems worldwide. Despite the global health catastrophe, especially in the number of infections and fatalities, the COVID-19 pandemic has also revolutionized research and discovery with remarkable success in diagnostics, treatments, and vaccine development. The use of many diagnostic methods has helped establish public health guidelines to mitigate the spread of COVID-19. However, limited information has been shared about these methods, and there is a need for the scientific community to learn about these technologies, in addition to their sensitivity, specificity, and limitations. This review article is focused on providing insights into the major methods used for SARS-CoV-2 detection. We describe in detail the core principle of each method, including molecular and serological approaches, along with reported claims about the rates of false negatives and false positives, the types of specimens needed, and the level of technology and the time required to perform each test. Although this study will not rank or prioritize these methods, the information will help in the development of guidelines and diagnostic protocols in clinical settings and reference laboratories.

Sensitive methods for detection of SARS-CoV-2 RNA

The occurrence of the COVID-19 pandemic caused by the SARS-CoV-2 virus since the end of 2019 has significantly affected the entire world. Now SARS-CoV-2 diagnostic tests are not only required for screening of suspected infected people for their medical treatment, but have also become a routine diagnosis for all people at a place where new cases have emerged in order to control spread of the disease from that region. For these reasons, sensitive methods for detection of SARS-CoV-2 are highly needed in order to avoid undetected infections. In addition, sample pooling that uses pooled specimens has been routinely employed as a time- and cost-effective strategy for community monitoring of SARS-CoV-2. In this regard, the content of each viral RNA sample of an individual will be further diluted in detection; therefore, higher detection sensitivity would be rather preferred. Among nucleic acid-based detection methods, isothermal nucleic acid amplifications are considered quite promising because they typically take less time to complete the test (even less than 20 min) without the need of thermal cycles. Hence, it does not necessitate the use of highly costly real-time PCR machines. According to recently published isothermal nucleic acid amplification methods, the reverse transcription recombinase polymerase amplification (RT-RPA) approach shows outstanding sensitivity with up to single-copy sensitivity in a test reaction. This chapter will mainly focus on how to employ RT-RPA technology to sensitively detect SARS-CoV-2 RNA. Besides, recently published RT-RPA based detection methods will be summarized and compared regarding their detection parameters and the primers and probes being used. In addition, we will also highlight the key considerations on how to design an ultrasensitive RT-RPA assay and the precautions needed to conduct the assay. Moreover, based on our recent report, we will also detail the methods we developed to detect SARS-CoV-2 RNA using modified RT-RPA, or RT-ERA, with single-copy sensitivity and the possible extensions beyond this method.

Effects of angiotensin receptor blockers and angiotensin-converting enzyme inhibitors on COVID-19

BACKGROUND

The World Health Organization reported that 28637952 people worldwide had been infected with severe acute respiratory syndrome coronavirus 2, the causative agent of coronavirus disease 2019 (COVID-19), by September 13.

AIM

The aim was to investigate whether long-term use of renin-angiotensin-aldosterone system (RAAS) inhibitors for the treatment of hypertension aggravates the performance of COVID-19 patients with hypertension.

METHODS

This was a retrospective analysis of lung computed tomography (CT) data and laboratory values of COVID-19 patients with hypertension who were admitted to Huoshenshan Hospital, Wuhan, Hubei Province, between February 18 and March 31, 2020. Patients were divided into two groups. Group A included 19 people who were long-term users of RAAS inhibitors for hypertension; and group B included 28 people who were randomly selected from the database and matched with group A by age, sex, basic diseases, and long-term use of other antihypertensive drugs. All patients underwent a series of CT and laboratory tests. We compared the most severe CT images of the two groups and the laboratory examination results within 2 d of the corresponding CT images.

RESULTS

The time until the most severe CT images from the onset of COVID-19 was 30.37 ± 14.25 d group A and 26.50 ± 11.97 d in group B. The difference between the two groups was not significant (t = 1.01, P = 0.32). There were no significant differences in blood laboratory values, C-reactive protein, markers of cardiac injury, liver function, or kidney function between the two groups. There was no significant difference in the appearance of the CT images between the two groups. The semiquantitative scores of each involved lobe were 11.84 ± 5.88 in group A and 10.36 ± 6.04 group B. The difference was not significantly different (t = 0.84, P = 0.41).

CONCLUSION

Chest CT is an important imaging tool to monitor the characteristics of COVID-19 and the degree of lung injury. Chronic use of RAAS inhibitors is not related to the severity of COVID-19, and it does not worsen the clinical process.

Rapid and Visual Detection of SARS-CoV-2 Using Multiplex Reverse Transcription Loop-Mediated Isothermal Amplification Linked With Gold Nanoparticle-Based Lateral Flow Biosensor

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has caused the outbreak of coronavirus disease 2019 (COVID-19) all over the world. In the absence of appropriate antiviral drugs or vaccines, developing a simple, rapid, and reliable assay for SARS-CoV-2 is necessary for the prevention and control of the COVID-19 transmission.

Methods

A novel molecular diagnosis technique, named multiplex reverse transcription loop-mediated isothermal amplification, that has been linked to a nanoparticle-based lateral flow biosensor (mRT-LAMP-LFB) was applied to detect SARS-CoV-2 based on the SARS-CoV-2 RdRp and N genes, and the mRT-LAMP products were analyzed using nanoparticle-based lateral flow biosensor. The mRT-LAMP-LFB amplification conditions, including the target RNA concentration, amplification temperature, and time were optimized. The sensitivity and specificity of the mRT-LAMP-LFB method were tested in the current study, and the mRT-LAMP-LFB assay was applied to detect the SARS-CoV-2 virus from clinical samples and artificial sputum samples.

Results

The SARS-CoV-2 specific primers based on the RdRp and N genes were valid for the establishment of mRT-LAMP-LFB assay to detect the SARS-CoV-2 virus. The multiple-RT-LAMP amplification condition was optimized at 63°C for 30 min. The full process, including reaction preparation, viral RNA extraction, RT-LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the mRT-LAMP-LFB technology was 20 copies per reaction. The specificity of mRT-LAMP-LFB detection was 100%, and no cross-reactions to other respiratory pathogens were observed.

Conclusion

The mRT-LAMP-LFB technique developed in the current study is a simple, rapid, and reliable method with great specificity and sensitivity when it comes to identifying SARS-CoV-2 virus for prevention and control of the COVID-19 disease, especially in resource-constrained regions of the world.

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.

COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, which has been a topic of major concern for global human health. The challenge to restrain the COVID-19 pandemic is further compounded by the emergence of several SARS-CoV-2 variants viz. B.1.1.7 (Alpha), B.1.351 (Beta), P1 (Gamma) and B.1.617.2 (Delta), which show increased transmissibility and resistance towards vaccines and therapies. Importantly, there is convincing evidence of increased susceptibility to SARS-CoV-2 infection among individuals with dysregulated immune response and comorbidities. Herein, we provide a comprehensive perspective regarding vulnerability of SARS-CoV-2 infection in patients with underlying medical comorbidities. We discuss ongoing vaccine (mRNA, protein-based, viral vector-based, etc.) and therapeutic (monoclonal antibodies, small molecules, plasma therapy, etc.) modalities designed to curb the COVID-19 pandemic. We also discuss in detail, the challenges posed by different SARS-CoV-2 variants of concern (VOC) identified across the globe and their effects on therapeutic and prophylactic interventions.

Which of us were more affected by the pandemic? The psychiatric impacts of the COVID-19 pandemic on healthcare professionals in the province where the first quarantine units were established in Turkey

INTRODUCTION

Psychiatric problems, such as stress and anxiety disorders, are encountered amongst healthcare professionals fighting epidemics. Considering that COVID-19 suddenly became a pandemic and healthcare professionals have not had access to sufficient information, it is a fact that healthcare professionals have been affected on a large scale. Heavy workloads, insufficient equipment and anxiety over families increase this impact. We aimed to investigate the extent to which healthcare professionals have been psychologically affected by COVID-19 and related factors.

METHODOLOGY

Data obtained through questionnaires completed by 348 healthcare professionals working during the COVID-19 pandemic and 350 participants who are in the control group were investigated. The Impact of Event Scale-revised (IES-R) for post-traumatic stress disorder (PTSD) and the Severity Index (ISI) for insomnia were used. Differences regarding gender, occupation, age group, marital status and sub-groups were statistically analysed.

RESULTS

Of the 348 healthcare professionals, 176 (50.6%) were women and 172 (49.4%) men, while 190 (54.6%) were doctors and 158 (45.4%) nurses. The incidence of PTSD was statistically significantly higher in the healthcare professionals group than in the control group (P < .001). The incidence of PTSD was statistically significantly higher amongst nurses (P = .001), women (P = .002) and those who were married (P = .007). Both PTSD and insomnia were found to be statistically significantly higher amongst those working in the "area of final diagnosis" (P = .016 and P = .002, respectively).

CONCLUSIONS

The determination of the groups most affected amongst professionals working in epidemics is important for the planning of in-service training and psychological support studies. If the fight against pandemics includes health teams with strong psychological grounding, it leads to qualified medical care for patients.

Effects of historical co-infection on host shift abilities of exploitative and competitive viruses

Rapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage ɸ6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that had experienced 300 generations of low MOI ecological history would be relatively advantaged in initial growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. However, the specific attributes of growth curves that supported their advantage differed by host, indicating interactions between both viral and host genotype. Although there will be host specificity in viral growth, we suggest based on infectivity differences of viruses from high versus low MOI histories that prior MOI selection can later affect emergence potential.

Cardiovascular Manifestations of COVID-19: Insights into a Single-Center Experience

Background  Since December 2019, an emerging outbreak of novel coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The aim of the present report is to describe a population with elevated levels of high-sensitive cardiac troponin T (hs-cTnT) and report on their management during the pandemic of COVID-19. Methods  In this retrospective cohort, we collected data from all patients with hs-cTnT levels of >50 ng/mL admitted to Fribourg Hospital between February 15, 2020, and April 15, 2020. The primary diagnosis for troponin elevation was recorded. Echocardiographic, electrocardiographic, and coronary angiographic data were analyzed for signs of myocardial ischemia, infarction, or other cardiomyopathies. In-hospital follow-up was performed for deaths from all causes and for cardiac deaths. Propensity score matching was used in a subgroup analysis to match COVID-19 and non-COVID-19 patients ( n  = 21 per group). Results  Overall, 215 patients with high hs-cTnT levels were enrolled. The median age was 75 [65-83] years and 30% were women. 21 patients (10%) were diagnosed with COVID-19. Of these, acute myocardial injury related to COVID-19 was the most commonly described cardiovascular manifestation during the pandemic peak. Median troponin values were not different between COVID-19 patients and non-COVID-19 patients (94 vs. 137, p  = 0.14). The number of cardiological examinations was globally low (echocardiography 51% and coronary angiography 52%) in the context of the pandemic. Patients in the COVID-19 group underwent significantly less echocardiographic examinations (19 vs. 55%, p ≤ 0.01) and coronary angiographies (5 vs. 58%, p ≤ 0.01) than non-COVID-19 patients. Overall mortality in patient with COVID-19 and elevated troponins was very high, as 38% of patients died during hospitalization including 14% for cardiac death. This trend was confirmed in the propensity score-matched analysis. Conclusion  Interpretation of troponins during the COVID-19 pandemic was complicated due to the low number of cardiovascular investigations in this context. Follow-up of patients with COVID-19 and cardiovascular events is important to assess their prognosis and to improve their care.

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data

Summary

The possibility that RNA transcripts from clinical samples contain plenty of virus RNAs has not been pursued actively so far. We here developed a new tool for analyzing virus-transcribed mRNAs, not virus copy numbers, in the data of bulk and single-cell RNA-sequencing of human cells. Our pipeline, named VIRTUS (VIRal Transcript Usage Sensor), was able to detect 762 viruses including herpesviruses, retroviruses and even SARS-CoV-2 (COVID-19), and quantify their transcripts in the sequence data. This tool thus enabled simultaneously detecting infected cells, the composition of multiple viruses within the cell, and the endogenous host-gene expression profile of the cell. This bioinformatics method would be instrumental in addressing the possible effects of covertly infecting viruses on certain diseases and developing new treatments to target such viruses.

Availability and implementation

: VIRTUS is implemented using Common Workflow Language and Docker under a CC-NC license. VIRTUS is freely available at https://github.com/yyoshiaki/VIRTUS.

Supplementary information

Supplementary data are available at Bioinformatics online.

The human microbiome and COVID-19: A systematic review

BACKGROUND

Human microbiotas are communities of microorganisms living in symbiosis with humans. They play an important role in the host immune response to respiratory viral infection. However, evidence on the human microbiome and coronavirus disease (COVID-19) relationship is insufficient. The aim of this systematic literature review was to evaluate existing evidence on the association between the microbiome and COVID-19 in humans and summarize these data in the pandemic era.

METHODS

We conducted a systematic literature review on the association between the microbiome and COVID-19 in humans by searching PubMed, Embase, and the Cochrane Library, CINAHL, and Web of Science databases for articles in English published up to October 31, 2020. The results were analyzed qualitatively. This study is registered with PROSPERO (CRD42020195982).

RESULTS

Of the 543 articles identified by searching databases, 16 in line with the research objectives were eligible for qualitative review: eight sampled the microbiome using stool, four using nasopharyngeal or throat swab, three using bronchoalveolar lavage fluid, and one using lung tissue. Fecal microbiome dysbiosis and increased opportunistic pathogens were reported in COVID-19 patients. Several studies suggested the dysbiosis in the lung microbiome of COVID-19 patients with an abundance of opportunistic pathogens using lower respiratory tract samples. The association between COVID-19 severity and the human microbiome remains uncertain.

CONCLUSION

The human fecal and respiratory tract microbiome changed in COVID-19 patients with opportunistic pathogen abundance. Further research to elucidate the effect of alternation of the human microbiome in disease pathogenesis is warranted.

Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here, we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole-genome represents a large number of potential co-mutations. In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5'UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly attenuated the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.

Urine Biochemical Parameters in Predicting Severity of SARS-CoV-2 Infection: an Experience in Tertiary Care Centre in Western India

BACKGROUND & OBJECTIVE

Coronavirus is an enveloped RNA virus that mainly causes respiratory infection. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) test of nasopharyngeal and oropharyngeal swab is the confirmatory diagnostic test for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection. The relationship between SARS-COV-2 and body fluid parameters is still not known. There have been few studies regarding the correlation between urine biochemical parameters and SARS-COV-2 infection. The aim of the study is to determine the importance of urinary biochemical parameters in SARS-COV-2 infection and whether these parameters can be used to predict the severity of the infection.

METHODS

This was a retrospective observational study consisting of total of 285 patients diagnosed with SARS-COV-2 infection. The patients were divided into three groups according to the severity of infection as mild (120 cases), moderate (110 cases) and severe (55 cases). During the study period 72 healthy persons were enrolled as controls. Analysis was done to find any relationship between various urine biochemical parameters and the severity of SARS-COV-2 infection.

RESULTS

Urinary occult blood (U. Blood) and Urinary protein (U. Pro) have higher positive rates in SARS-COV-2 patients as compared with healthy controls. Among the severities of SARS-COV-2 infection (mild, moderate and severe), both these parameters were significantly higher. Glucose (Glu) and Ketone (Ket) positivity rate was more in moderate cases of SARS-COV-2 than mild cases.

CONCLUSION

Urinary biochemical parameters are very useful in identification of SARS-COV-2 infection and also have the advantage in evaluating the progression in patients infected with SARS-COV-2. Among the different parameters, Urinary Occult Blood and Urinary protein are significant in the differentiation of SARS-COV-2 severity.

Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry

With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical-medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.

Prognostic value of three rapid scoring scales and combined predictors for the assessment of patients with coronavirus disease 2019

Aim

To explore the factors affecting mortality in patients with COVID‐19 and to verify the predictive value of the three rapid scoring scales MEWS, RAPS and REMS.

Design

Cross‐sectional observational study.

Methods

Kaplan–Meier and Cox survival analyses were performed to identify the risk factors associated with COVID‐19‐related death. A ROC curve analysis was used to evaluate the abilities of the three scoring scales to predict the prognosis of COVID‐19 patients.

Results

Age, low blood oxygen saturation level and decreased lymphocyte count were the high risk factors for COVID‐19‐related mortality. The analysis of the abilities of the three scales to predict the prognosis of COVID‐19 patients: The AUC of 0.641 for the RAPS (p = .065). The MEWS (AUC = 0.705, p = .007), compared with RAPS, the NRI was 0.371(p = .03), and the IDI = 0.092 (p = .046); The REMS (AUC = 0.841, p < .001), compared with MEWS, the NRI was 0.227(p = .12), and the IDI=0.09(p = .047); The Combining Predictor (AUC = 0.878, p < .001), compared with REMS, the NRI was 0.25(p = .113), and the IDI=0.02(p = .598).

Conclusion

Patients with an old age, low blood oxygen saturation level and decreased lymphocyte count were at a high risk of COVID‐19‐related mortality. Moreover, our analysis revealed that the REMS had a better prognostic ability than the MEWS and RAPS when applied to COVID‐19 patients. Our findings suggest that the REMS can be used as a rapid scoring tool for the early assessment of COVID‐19 severity.

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.

A review on COVID-19 for medical students

It has not been very long since the SARS-CoV 2002 and MERS-CoV 2012 epidemics. Yet again, nature has introduced SARS-CoV-2, also known as COVID-19, a highly virulent strain of the coronavirus that has its origin in the city of Wuhan, Hubei Province, China. Primarily, a zoonotic infection, the virus probably found its way to humans through infected wild bats sold in the Wuhan local market. What makes the virus virulent, is its ability to infect multiple people at once through single index case. This has led to inability to contain the virus with ease posing a significant threat to national and international health-care resources and economies. The objective of this review is to highlight the key features of the novel CoV-19 infection as per existing data for better understanding of the disease.

Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients' Clinical Sub-Phenotype

Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-infecting respiratory pathogens in the nasopharyngeal tract of SARS-CoV-2 positive patients. Two complementary metagenomics based sequencing approaches, Respiratory Virus Oligo Panel (RVOP) and Holo-seq, were utilized for unbiased detection of co-infecting viruses and bacteria. The limited SARS-CoV-2 clade diversity along with differential clinical phenotype seems to be partially explained by the observed spectrum of co-infections. We found a total of 43 bacteria and 29 viruses amongst the patients, with 18 viruses commonly captured by both the approaches. In addition to SARS-CoV-2, Human Mastadenovirus, known to cause respiratory distress, was present in a majority of the samples. We also found significant differences of bacterial reads based on clinical phenotype. Of all the bacterial species identified, ∼60% have been known to be involved in respiratory distress. Among the co-pathogens present in our sample cohort, anaerobic bacteria accounted for a preponderance of bacterial diversity with possible role in respiratory distress. Clostridium botulinum, Bacillus cereus and Halomonas sp. are anaerobes found abundantly across the samples. Our findings highlight the significance of metagenomics based diagnosis and detection of SARS-CoV-2 and other respiratory co-infections in the current pandemic to enable efficient treatment administration and better clinical management. To our knowledge this is the first study from India with a focus on the role of co-infections in SARS-CoV-2 clinical sub-phenotype.

SARS-CoV-2's claimed natural origin is undermined by issues with genome sequences of its relative strains: Coronavirus sequences RaTG13, MP789 and RmYN02 raise multiple questions to be critically addressed by the scientific community

RaTG13, MP789, and RmYN02 are the strains closest to SARS‐CoV‐2, and their existence came to light only after the start of the pandemic. Their genomes have been used to support a natural origin of SARS‐CoV‐2 but after a close examination all of them exhibit several issues. We specifically address the presence in RmYN02 and closely related RacCSxxx strains of a claimed natural PAA/PVA amino acid insertion at the S1/S2 junction of their spike protein at the same position where the PRRA insertion in SARS‐CoV‐2 has created a polybasic furin cleavage site. We show that RmYN02/RacCSxxx instead of the claimed insertion carry a 6‐nucleotide deletion in the region and that the 12‐nucleotide insertion in SARS‐CoV‐2 remains unique among Sarbecoviruses. Also, our analysis of RaTG13 and RmYN02's metagenomic datasets found unexpected reads which could indicate possible contamination. Because of their importance to inferring SARS‐CoV‐2′s origin, we call for a careful reevaluation of RaTG13, MP789 and RmYN02 sequencing records and assembly methods.

Significant variations across European centres in implementing recommended guidelines for the paediatric gastroenterology endoscopy suite during the COVID-19 pandemic

Supplemental Digital Content is available in the text.

The European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) published recommendations regarding protection for the paediatric endoscopist during the coronavirus 2019 (COVID-19) pandemic.The aim of this survey was to investigate whether European paediatric gastroenterology centres applied the recommendations and how this extraordinary situation was handled by the different centres.

New Approaches and Repurposed Antiviral Drugs for the Treatment of the SARS-CoV-2 Infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19). The outbreak of this coronavirus was first identified in Wuhan (Hubei, China) in December 2019, and it was declared as pandemic by the World Health Organization (WHO) in March 2020. Today, several vaccines against SARS-CoV-2 have been approved, and some neutralizing monoclonal antibodies are being tested as therapeutic approaches for COVID-19 but, one of the key questions is whether both vaccines and monoclonal antibodies could be effective against infections by new SARS-CoV-2 variants. Nevertheless, there are currently more than 1000 ongoing clinical trials focusing on the use and effectiveness of antiviral drugs as a possible therapeutic treatment. Among the classes of antiviral drugs are included 3CL protein inhibitors, RNA synthesis inhibitors and other small molecule drugs which target the ability of SARS-COV-2 to interact with host cells. Considering the need to find specific treatment to prevent the emergent outbreak, the aim of this review is to explain how some repurposed antiviral drugs, indicated for the treatment of other viral infections, could be potential candidates for the treatment of COVID-19.

The understanding of the immunopathology in COVID-19 infection

Coronaviruses belonging to the Coronaviridae family are single-stranded RNA viruses. The entry of SARS-CoV-2 is accomplished via ACE-2 receptors. SARS-CoV-2 infection coactivates both innate and adaptive immune responses. Although SARS-CoV-2 stimulates antibody production with a typical pattern of IgM/IgG, cellular immunity is also impaired. In severe cases, low CD4 + and CD8 + T cell counts are associated with impaired immune functions, and high neutrophil/lymphocyte ratios accompanying low lymphocyte subsets have been demonstrated. Recently, high IFN -α/γ ratios with impaired T cell responses, and increased IL-1, IL-6, TNF-α, MCP-1, IP-10, IL-4, IL-10 have been reported in COVID-19 infection. Increased proinflammatory cytokines and chemokines in patients with severe COVID-19 may cause the suppression of CD4 + and CD8 + T cells and regulatory T cells, causing excessive inflammatory responses and fatal cytokine storm with tissue and organ damage. Consequently, novel therapeutics to be developed against host immune system, including blockade of cytokines (IL-6, IL-1, IFN) themselves, their receptors or signaling pathways- JAK inhibitors- could be effective as potential therapeutics.

Clinical Characteristics of Foreign-Imported COVID-19 Cases in Xi'an, China

Background

Effective management of foreign-imported COVID-19 cases is a new and great challenge for China. Our study focused on the foreign-imported COVID-19 cases to provide detailed data for insights into the prevention, early diagnosis, treatment and control of imported COVID-19.

Methods

For this observational and retrospective study, we investigated the clinical characteristics of imported COVID-19 cases that were confirmed by real-time RT-PCR in the Xi’an Public Health Center from 29 March 2020 to 31 August 2020.

Results

Of the 79 patients with COVID-19, 19 (24.1%) had exposure to confirmed COVID-19 patients, 15 (19.0%) had exposure to suspicious COVID-19 patients, and 45 (56.9%) had an unclear history of exposure to confirmed patients. The mean age of the patients was 38 years, and 70 (88.7%) patients were male. Except for 2 severe cases, the remaining 58 (73.4%) cases displayed mild or moderate symptoms, and 19 (24.2%) infected patients were asymptomatic. Twenty-one (26.6%) patients were not diagnosed until a third or later nucleic acid test. Ten (12.7%) patients had chronic diseases. The most common manifestations of the patients were cough [18 (22.8%) cases], fever [9 (11.4%) cases] and sore throat [9 (11.4%) cases]. Forty-one (51.9%) cases showed abnormal chest CT images, To date, all patients have been discharged, and no patient has died.

Conclusion

The imported COVID-19 cases in Xi’an were mainly young and middle-aged adults with mild or moderate symptoms who had a low rate of comorbidity, showed favourable laboratory and chest CT images, and had a better prognosis. Notably, for suspected COVID-19 cases, at least three consecutive nucleic acid tests should be carried out to avoid missed detection of infected patients. Except for severe cases, high-level medical resources are not necessary in most cases.

Comparative Immunomodulatory Evaluation of the Receptor Binding Domain of the SARS-CoV-2 Spike Protein; a Potential Vaccine Candidate Which Imparts Potent Humoral and Th1 Type Immune Response in a Mouse Model

The newly emerged novel coronavirus, SARS-CoV-2, the causative agent of COVID-19 has proven to be a threat to the human race globally, thus, vaccine development against SARS-CoV-2 is an unmet need driving mass vaccination efforts. The receptor binding domain of the spike protein of this coronavirus has multiple neutralizing epitopes and is associated with viral entry. Here we have designed and characterized the SARS-CoV-2 spike protein fragment 330-526 as receptor binding domain 330-526 (RBD330-526) with two native glycosylation sites (N331 and N343); as a potential subunit vaccine candidate. We initially characterized RBD330-526 biochemically and investigated its thermal stability, humoral and T cell immune response of various RBD protein formulations (with or without adjuvant) to evaluate the inherent immunogenicity and immunomodulatory effect. Our result showed that the purified RBD immunogen is stable up to 72 h, without any apparent loss in affinity or specificity of interaction with the ACE2 receptor. Upon immunization in mice, RBD generates a high titer humoral response, elevated IFN-γ producing CD4+ cells, cytotoxic T cells, and robust neutralizing antibodies against live SARS-CoV-2 virus. Our results collectively support the potential of RBD330-526 as a promising vaccine candidate against SARS-CoV-2.

The SARS-CoV-2 subgenome landscape and its novel regulatory features

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate negative subgenomes (subgenomic RNAs [sgRNAs]) through transcription-regulating sequence (TRS)-dependent template switching, but the global dynamic landscapes of coronaviral subgenomes and regulatory rules remain unclear. Here, using next-generation sequencing (NGS) short-read and Nanopore long-read poly(A) RNA sequencing in two cell types at multiple time points after infection with SARS-CoV-2, we identified hundreds of template switches and constructed the dynamic landscapes of SARS-CoV-2 subgenomes. Interestingly, template switching could occur in a bidirectional manner, with diverse SARS-CoV-2 subgenomes generated from successive template-switching events. The majority of template switches result from RNA-RNA interactions, including seed and compensatory modes, with terminal pairing status as a key determinant. Two TRS-independent template switch modes are also responsible for subgenome biogenesis. Our findings reveal the subgenome landscape of SARS-CoV-2 and its regulatory features, providing a molecular basis for understanding subgenome biogenesis and developing novel anti-viral strategies.

The human pandemic coronaviruses on the show: The spike glycoprotein as the main actor in the coronaviruses play

Three coronaviruses (CoVs) have threatened the world population by causing outbreaks in the last two decades. In late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged and caused the coronaviruses to disease 2019 (COVID-19), leading to the ongoing global outbreak. The other pandemic coronaviruses, SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV), share a considerable level of similarities at genomic and protein levels. However, the differences between them lead to distinct behaviors. These differences result from the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which plays an essential role in coronavirus infection, pathogenicity, transmission, and evolution. In this review, we brought together many studies narrating a sequence of events and highlighting the differences among S proteins from SARS-CoV, MERS-CoV, and SARS-CoV-2. It was performed here, analysis of S protein sequences and structures from the three pandemic coronaviruses pointing out the mutations among them and what they come through. Additionally, we investigated the receptor-binding domain (RBD) from all S proteins explaining the mutation and biological importance of all of them. Finally, we discuss the mutation in the S protein from several new isolates of SARS-CoV-2, reporting their difference and importance. This review brings into detail how the variations in S protein that make SARS-CoV-2 more aggressive than its relatives coronaviruses and other differences between coronaviruses.

Molecular Insights into COVID-19 Pathophysiology, Immune Pathogenesis, Detection, and Treatment

In late December 2019, a new kind of Coronavirus called severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) was officially identified in Wuhan, China. In March 2020, SARS-CoV-2 was declared a pandemic by the World Health Organization (WHO), and it has infected millions of people worldwide. SARS-CoV-2 is a highly contagious Coronavirus, which has led to an outbreak of acute respiratory tract infection called "Coronavirus disease 2019" (COVID-19), resulting in mild to severe respiratory infections in humans. The design of appropriate therapeutic approaches is dependent on the understanding of molecular and cellular pathways of Coronavirus infections. In this study, we summarized the characteristic features of SARS-CoV-2. In addition, we considered the recent information regarding COVID-19 molecular immune pathogenesis, diagnosis, and potential treatment, which may provide novel perspectives and therapeutic goals in combating SARS-CoV-2.

Betulonic Acid Derivatives Interfering with Human Coronavirus 229E Replication via the nsp15 Endoribonuclease

To develop antiviral therapeutics against human coronavirus (HCoV) infections, suitable coronavirus drug targets and corresponding lead molecules must be urgently identified. Here, we describe the discovery of a class of HCoV inhibitors acting on nsp15, a hexameric protein component of the viral replication-transcription complexes, endowed with immune evasion-associated endoribonuclease activity. Structure-activity relationship exploration of these 1,2,3-triazolo-fused betulonic acid derivatives yielded lead molecule 5h as a strong inhibitor (antiviral EC50: 0.6 μM) of HCoV-229E replication. An nsp15 endoribonuclease active site mutant virus was markedly less sensitive to 5h, and selected resistance to the compound mapped to mutations in the N-terminal part of HCoV-229E nsp15, at an interface between two nsp15 monomers. The biological findings were substantiated by the nsp15 binding mode for 5h, predicted by docking. Hence, besides delivering a distinct class of inhibitors, our study revealed a druggable pocket in the nsp15 hexamer with relevance for anti-coronavirus drug development.

Exploring antibody repurposing for COVID-19: beyond presumed roles of therapeutic antibodies

The urgent need for a treatment of COVID-19 has left researchers with limited choice of either developing an effective vaccine or identifying approved/investigational drugs developed for other medical conditions for potential repurposing, thus bypassing long clinical trials. In this work, we compared the sequences of experimentally verified SARS-CoV-2 neutralizing antibodies and sequentially/structurally similar commercialized therapeutic monoclonal antibodies. We have identified three therapeutic antibodies, Tremelimumab, Ipilimumab and Afasevikumab. Interestingly, these antibodies target CTLA4 and IL17A, levels of which have been shown to be elevated during severe SARS-CoV-2 infection. The candidate antibodies were evaluated further for epitope restriction, interaction energy and interaction surface to gauge their repurposability to tackle SARS-CoV-2 infection. Our work provides candidate antibody scaffolds with dual activities of plausible viral neutralization and immunosuppression. Further, these candidate antibodies can also be explored in diagnostic test kits for SARS-CoV-2 infection. We opine that this in silico workflow to screen and analyze antibodies for repurposing would have widespread applications.

COVID-19 one year later: a retrospect of CRISPR-Cas system in combating COVID-19

Coronavirus disease 2019 (COVID-19), an infectious disease caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a persistent global threat. The transmission of SARS-CoV-2 is wide and swift. Rapid detection of the viral RNA and effective therapy are imperative to prevent the worldwide spread of the new infectious disease. Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR)- CRISPR-associated protein (Cas) system is an RNA-directed adaptive immune system, and it has been transformed into a gene editing tool. Applications of CRISPR-Cas system involves in many fields, such as human gene therapy, drug discovery and disease diagnosis. Under the background of COVID-19 pandemic, CRISPR-Cas system shows hidden capacity to fight the emergency in many aspects. This review will focus on the role of gene editing in COVID-19 diagnosis and treatment. We will describe the potential use of CRISPR-Cas-based system in combating COVID-19, from diagnosis to treatment. Furthermore, the limitation and perspectives of this novel technology are also evaluated.

Design and synthesis of pyrazolone-based compounds as potent blockers of SARS-CoV-2 viral entry into the host cells

SARS-CoV-2 are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. It relies on the fusion of their envelope with the host cell membrane to deliver their nucleocapsid into the host cell. The spike glycoprotein (S) mediates virus entry into cells via the human Angiotensin-converting enzyme 2 (hACE2) protein located on many cell types and tissues' outer surface. This study, therefore, aimed to design and synthesize novel pyrazolone-based compounds as potential inhibitors that would interrupt the interaction between the viral spike protein and the host cell receptor to prevent SARS-CoV 2 entrance into the cell. A series of pyrazolone compounds as potential SARS-CoV-2 inhibitors were designed and synthesized. Employing computational techniques, the inhibitory potentials of the designed compounds against both spike protein and hACE2 were evaluated. Results of the binding free energy from the in-silico analysis, showed that three compounds (7i, 7k and 8f) and six compounds (7b, 7h, 7k, 8d, 8g, and 8h) showed higher and better binding high affinity to SARS-CoV-2 Sgp and hACE-2, respectively compared to the standard drugs cefoperazone (CFZ) and MLN-4760. Furthermore, the outcome of the structural analysis of the two proteins upon binding of the inhibitors showed that the two proteins (SARS-CoV-2 Sgp and hACE-2) were stable, and the structural integrity of the proteins was not compromised. This study suggests pyrazolone-based compounds might be potent blockers of the viral entry into the host cells.

Probiotic-Based Vaccines May Provide Effective Protection against COVID-19 Acute Respiratory Disease

Severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) infection, the causative agent of COVID-19, now represents the sixth Public Health Emergency of International Concern (PHEIC)—as declared by the World Health Organization (WHO) since 2009. Considering that SARS-CoV-2 is mainly transmitted via the mucosal route, a therapy administered by this same route may represent a desirable approach to fight SARS-CoV-2 infection. It is now widely accepted that genetically modified microorganisms, including probiotics, represent attractive vehicles for oral or nasal mucosal delivery of therapeutic molecules. Previous studies have shown that the mucosal administration of therapeutic molecules is able to induce an immune response mediated by specific serum IgG and mucosal IgA antibodies along with mucosal cell-mediated immune responses, which effectively concur to neutralize and eradicate infections. Therefore, advances in the modulation of mucosal immune responses, and in particular the use of probiotics as live delivery vectors, may encourage prospective studies to assess the effectiveness of genetically modified probiotics for SARS-CoV-2 infection. Emerging trends in the ever-progressing field of vaccine development re-emphasize the contribution of adjuvants, along with optimization of codon usage (when designing a synthetic gene), expression level, and inoculation dose to elicit specific and potent protective immune responses. In this review, we will highlight the existing pre-clinical and clinical information on the use of genetically modified microorganisms in control strategies against respiratory and non-respiratory viruses. In addition, we will discuss some controversial aspects of the use of genetically modified probiotics in modulating the cross-talk between mucosal delivery of therapeutics and immune system modulation.

Drug Repurposing of Itraconazole and Estradiol Benzoate against COVID-19 by Blocking SARS-CoV-2 Spike Protein-Mediated Membrane Fusion

SARS-CoV-2 caused the emerging epidemic of coronavirus disease in 2019 (COVID-19). To date, there are more than 82.9 million confirmed cases worldwide, there is no clinically effective drug against SARS-CoV-2 infection. The conserved properties of the membrane fusion domain of the spike (S) protein across SARS-CoV-2 make it a promising target to develop pan-CoV therapeutics. Herein, two clinically approved drugs, Itraconazole (ITZ) and Estradiol benzoate (EB), are found to inhibit viral entry by targeting the six-helix (6-HB) fusion core of SARS-CoV-2 S protein. Further studies shed light on the mechanism that ITZ and EB can interact with the heptad repeat 1 (HR1) region of the spike protein, to present anti-SARS-CoV-2 infections in vitro, indicating they are novel potential therapeutic remedies for COVID-19 treatment. Furthermore, ITZ shows broad-spectrum activity targeting 6-HB in the S2 subunit of SARS-CoV and MERS-CoV S protein, inspiring that ITZ have the potential for development as a pan-coronavirus fusion inhibitor.

Mid-regional pro-atrial natriuretic peptide independently predicts short-term mortality in COVID-19

BACKGROUND

Mid-regional pro-atrial natriuretic peptide (MR-proANP) is a strong prognostic marker in several inflammatory, respiratory and cardiovascular conditions, but has not been studied in COVID-19 yet.

METHODS

This prospective, observational study of patients with COVID-19 infection was conducted from 6 June to 26 November 2020 in different wards of a tertiary hospital. MR-proANP, N-terminal pro-brain natriuretic peptide (NT-proBNP) and high-sensitive cardiac troponin I levels on admission were collected and tested for their association with disease severity and 28-day mortality.

RESULTS

A total of 213 eligible patients with COVID-19 were included in the final analyses of whom 13.2% (n = 28) died within 28 days. Median levels of MR-proANP at admission were significantly higher in nonsurvivors (307 pmol/L IQR, [161 - 532] vs 75 pmol/L [IQR, 43 - 153], P < .001) compared to survivors and increased with disease severity and level of hypoxaemia. The area under the ROC curve for MR-proANP predicting 28-day mortality was 0.832 (95% CI 0.753 - 0.912, P < .001). An optimal cut-off point of 160 pmol/L yielded a sensitivity of 82.1% and a specificity of 76.2%. MR-proANP was a significant predictor of 28-day mortality independent of clinical confounders, comorbidities and established prognostic markers of COVID-19 (HR 2.77, 95% CI 1.21 - 6.37; P = .016), while NT-proBNP failed to independently predict 28-day mortality and had a numerically lower AUC compared to MR-proANP.

CONCLUSION

Higher levels of MR-proANP at admission are associated with disease severity of COVID-19 and act as a powerful and independent prognostic marker of 28-day mortality.

SARS-CoV-2-Seronegative Subjects Target CTL Epitopes in the SARS-CoV-2 Nucleoprotein Cross-Reactive to Common Cold Coronaviruses

The beta-coronavirus SARS-CoV-2 induces severe disease (COVID-19) mainly in elderly persons with risk factors, whereas the majority of patients experience a mild course of infection. As the circulating common cold coronaviruses OC43 and HKU1 share some homologous sequences with SARS-CoV-2, beta-coronavirus cross-reactive T-cell responses could influence the susceptibility to SARS-CoV-2 infection and the course of COVID-19. To investigate the role of beta-coronavirus cross-reactive T-cells, we analyzed the T-cell response against a 15 amino acid long peptide (SCoV-DP15: DLSPRWYFYYLGTGP) from the SARS-CoV-2 nucleoprotein sequence with a high homology to the corresponding sequence (QLLPRWYFYYLGTGP) in OC43 and HKU1. SCoV-DP15-specific T-cells were detected in 4 out of 23 (17.4%) SARS-CoV-2-seronegative healthy donors. As HIV-1 infection is a potential risk factor for COVID-19, we also studied a cohort of HIV-1-infected patients on antiretroviral therapy. 44 out of these 116 HIV-1-infected patients (37.9%) showed a specific recognition of the SCoV-DP15 peptide or of shorter peptides within SCoV-DP15 by CD4+ T-cells and/or by CD8+ T-cells. We could define several new cross-reactive HLA-I-restricted epitopes in the SARS-CoV-2 nucleoprotein such as SPRWYFYYL (HLA-B*07, HLA-B*35), DLSPRWYFYY (HLA-A*02), LSPRWYFYY (HLA-A*29), WYFYYLGTGP and WYFYYLGT. Epitope specific CD8+ T-cell lines recognized corresponding epitopes within OC43 and HKU1 to a similar degree or even at lower peptide concentrations suggesting that they were induced by infection with OC43 or HKU1. Our results confirm that SARS-CoV-2-seronegative subjects can target SARS-CoV-2 not only by beta-coronavirus cross-reactive CD4+ T-cells but also by cross-reactive CD8+ cytotoxic T-cells (CTL). The delineation of cross-reactive T-cell epitopes contributes to an efficient epitope-specific immunomonitoring of SARS-CoV-2-specific T-cells. Further prospective studies are needed to prove a protective role of cross-reactive T-cells and their restricting HLA alleles for control of SARS-CoV-2 infection. The frequent observation of SARS-CoV-2-reactive T-cells in HIV-1-infected subjects could be a reason that treated HIV-1 infection does not seem to be a strong risk factor for the development of severe COVID-19.

Predicted impacts of government policies and actions on the SARS-CoV-2 disease in the northwestern Himalayan region, India

AIM

The outbreak of the new coronavirus pandemic (SARS-CoV-2) was initiated in December 2019, and within a couple of months it became a global health emergency. Given the importance to assess the evolution and transmissibility of SARS-CoV-2 and to forecast the next scenario of the pandemic, mainly in countries with limited healthcare systems, we estimated the reproductive number (R0) of SARS-CoV-2 in Jammu and Kashmir (J&K), India, and a possible scenario for this pandemic in the region.

SUBJECT AND METHODS

We estimated the reproductive number (R0) of SARS-CoV-2 in its first outbreak stage in the northwestern region of Himalaya, India, and we also predicted new daily cases for the next 90 days using different R0, testing a plausible end of the SARS-CoV-2 outbreak.

RESULTS

Our results showed a considerable increase in the number of cases, but with a tendency to asymptote. Anantnag, Bandipora, Baramulla, Shopian, and Srinagar districts showed more than 100 cases and Kulgam and Kathua districts showed strong growth of the number of cases from the beginning of May, without a tendency to normalization. The estimated R0 for the J&K region was 1.041; but by decreasing the RO by 10, 25, and 50%, we observed a great decrease in the daily number of new cases, especially by decreasing by 50%.

CONCLUSION

In this study, we indicate positive effects of the preventive measures, such as lockdown and social distancing, taken in the J&K region, showing a stabilization of the growth curves of new cases of SARS-CoV-2, which tends to a strong decrease over time as the R0 decreases.

Performance evaluation of Truenat™ Beta CoV & Truenat™ SARS-CoV-2 point-of-care assays for coronavirus disease 2019

Background & objectives:

The rapid diagnosis of coronavirus disease 2019 (COVID-19) is a significant step towards the containment of the virus. The surge of COVID-19 cases in India and across the globe necessitates a rapid and sensitive molecular assay. Rapid point-of-care (PoC) assays (Truenat Beta CoV and Truenat SARS-CoV-2 assays) for the diagnosis of COVID-19 have been developed which are expected to shorten the turnaround time of reporting of results and also can be used for field investigations of COVID-19. The objectives of the study were to validate the performance of Truenat Beta CoV and Truenat SARS-CoV-2 PoC assays for the detection of SARS-CoV-2 infected cases with reference to analytical sensitivity, precision/inter-machine variation, clinical sensitivity and clinical specificity.

Methods:

The rapid PoC screening and confirmatory assays were prospectively validated at the State Level Virus Research and Diagnostic Laboratory at Bangalore Medical College and Research Institute, Bengaluru, under technical supervision by the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune. Real-time reverse transcription-polymerase chain reaction (rRT-PCR) was considered as the reference standard against which the rapid assays were validated for all samples tested based on analytical sensitivity, precision/inter-machine variation, clinical sensitivity and clinical specificity.

Results:

Truenat Beta CoV and Truenat SARS-CoV-2 assays showed concordant results when compared with the reference standard rRT-PCR. These PoC assays exhibited 100 per cent sensitivity, specificity, positive predictive value and negative predictive value.

Interpretation & conclusions:

Truenat Beta CoV and Truenat SARS-CoV-2 assays showed concordance with the reference standard assay and may be recommended for screening and confirmation of SARS-CoV-2 in the field settings.