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

The antigenic anatomy of SARS-CoV-2 receptor binding domain

Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50 < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

The relationship between nutritional status and the prognosis of COVID-19: A retrospective analysis of 63 patients

It is important for patients to maintain a good nutritional status as a health promotion strategy to improve the immune function and thus the prognosis of coronavirus disease 2019 (COVID-19).The objective of this retrospective study is to analyze the relationships of nutritional status with inflammation levels, protein reserves, baseline immune status, severity, length of hospital stay, and prognosis of COVID-19 patients.A total of 63 COVID-19 patients hospitalized in the People's Hospital and the Traditional Chinese Medicine Hospital of the Xinzhou District, Wuhan, China, from January 29, 2020 to March 17, 2020. Sixty-three patients were divided into 3 groups according to the guidelines, moderate (n = 22), severe (n = 14), and critical (n = 25), respectively. The differences in the total nutrition risk screening (NRS) score, inflammation level, protein reserve, baseline immune status, length of hospital stay, and prognosis were compared among patients with moderate, severe, and critical COVID-19.Patients with higher NRS scores tend to have more severe COVID-19, higher C-reactive protein and serum procalcitonin levels, higher white blood cell counts, lower lymphocyte counts, and higher mortality rates (P < .05).Nutritional status may be an indirect factor of the severity and prognosis of COVID-19.

A comprehensive review and update on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Coronavirus disease 2019 (COVID-19): what do we know now in 2021?

It has been more than a year since the new virus called severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) was identified in Wuhan, China. The disease it causes was named Coronavirus disease 2019 (COVID-19), and on 11 March 2020 it was declared a pandemic. As the virus continues to spread, the number of patients worldwide has already crossed the 100 million mark with more than 2 million deaths. We sought to provide an update on the progress made in identifying the virus, its pathophysiology, risk factors such as hypertension, diabetes, and smoking, as well as various methods of treatment. Our review also provided an overview of the different vaccines.

False-positive colloidal gold-based immunochromatographic strip assay reactions for antibodies to SARS-CoV-2 in patients with autoimmune diseases

BACKGROUND

The outbreak of the novel 2019 coronavirus disease (COVID-19) was declared a global pandemic by the World Health Organization (WHO) on March 11, 2020. The diagnosis of COVID-19 is frequently based on a positive serological test. We noted the occurrence of false-positive results for COVID-19 in the colloidal gold-based immunochromatographic strip (ICS) assay in sera from patients with autoimmune diseases (ADs). This study aimed to evaluate the possible reasons for the false-positive results in two ICS assays (Wondfo ICS and Innovita ICS) and to investigate the effect of urea dissociation in reducing false-positive results.

METHODS

The sera of 135 patients with ADs, 13 confirmed COVID-19 patients, 95 disease controls, and 120 healthy controls were tested for immunoglobin M (IgM) and IgG against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Wondfo and Innovita ICS kits. The distributions of auto-antibodies in antibody-positive and antibody-negative groups were also compared, and bivariable logistic regression was used to assess auto-antibodies associated with false-positive results. A urea dissociation test of ICS was performed for the SARS-CoV-2 antibody-positive samples.

RESULTS

Specificity of Wondfo ICS for the 95 disease controls was 94.74% compared to 98.95% and 96.84% for Innovita SARS-CoV-2 IgM and IgG, respectively. Specificity of Wondfo ICS for the 120 healthy controls was 97.5% compared to 100% and 99.17% for Innovita SARS-CoV-2 IgM and IgG, respectively. Specificity of Wondfo ICS for AD patients was 73.33% compared to 97.78% and 96.30% for Innovita SARS-CoV-2 IgM and IgG, respectively. Sensitivity was 74.07% for Wondfo compared to 70.37% for Innovita IgM and 66.67% for Innovita IgG. Using the Wondfo ICS, the percentage of elevated rheumatoid factor (RF) level (>20 IU/mL) was higher in the SARS-CoV-2 antibody-positive group compared with the antibody-negative group [27/36 (75.0%) vs. 34/99 (34.34%), P=0.001]. The elevated RF was associated with antibody positivity, with an odds ratio of 4.671 [95% confidence interval (CI), 1.88-11.69]. The specificity of the Wondfo ICS assay for the AD patients was increased from 73.33% to 94.07% after the urea dissociation assay.

CONCLUSIONS

An elevated serum RF level could lead to false-positive results when detecting SARS-CoV-2 antibodies using the Wondfo ICS kit, and the urea dissociation assay would be helpful in reducing the incidence of false-positive results.

Potential role of viral metagenomics as a surveillance tool for the early detection of emerging novel pathogens

Since the early times, human beings have always been faced with deadly microbial infections, both bacterial and viral. Pathogens such as viruses are always evolving owing to the processes of antigenic shift and drift. Such viral evolution results in the emergence of new types and serovars that prove deadly for humans-like influenza pandemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The pandemic of novel coronavirus SARS-CoV-2 is the recent example. It has resulted in a great loss of human lives and a serious burden on economy across the globe. To counter such situations, a system should exist for the early detection of emerging viral pathogens. This will help prevent possible outbreaks and save human lives. Most of such deadly novel viruses and viral outbreaks are known to be originated from animal hosts. Regular monitoring of potential hot spots of such emerging microbes, such as zoos and animal markets, through metagenomics could help assess the presence of new viruses and pathogens. In this review, we focus on the potential of viral metagenomics and propose a surveillance system based on it for the early detection and hence prevention of such emerging viral infections.

Exploratory assessment of the occurrence of SARS-CoV-2 in aerosols in hospital facilities and public spaces of a metropolitan center in Brazil

Although much has been discovered regarding the characteristics of SARS-CoV-2, its presence in aerosols and their implications in the context of the pandemic is still controversial. More research on this topic is needed to contribute to these discussions. Presented herein are the results of ongoing research to detect SARS-CoV-2 RNA in aerosol in different hospital facilities (indoor environments) and public spaces (outdoor environments) of a metropolitan center in Brazil. From May to August 2020, 62 samples were collected using active sampling method (air samplers with filters) and passive method (petri dishes) in two hospitals, with different occupancies and infrastructure for contamination control. Outdoor public spaces such as sidewalks and a bus station were also investigated. Five air samples from four facilities in a hospital tested positive for SARS-CoV-2 in suspended and sedimentable particles. SARS-CoV-2 was found in aerosols inside the Intensive Care Unit (ICU), in the protective apparel removal room, in the room containing patient mobile toilets and used clothes (room with natural ventilation) and in an external corridor adjacent to the ICU, probably coming from infected patients and/or from aerosolization of virus-laden particles on material/equipment. Our findings reinforce the hypothesis of airborne transmission of the new coronavirus, contributing to the planning of effective practices for pandemic control.

COVID-19 and human reproduction: A pandemic that packs a serious punch

The COVID-19 pandemic has led to a worldwide health emergency that has impacted 188 countries at last count. The rapid community transmission and relatively high mortality rates with COVID-19 in modern times are relatively unique features of this flu pandemic and have resulted in an unparalleled global health crisis. SARS-CoV-2, being a respiratory virus, mainly affects the lungs, but is capable of infecting other vital organs, such as brain, heart and kidney. Emerging evidence suggests that the virus also targets male and female reproductive organs that express its main receptor ACE2, although it is as yet unclear if this has any implications for human fertility. Furthermore, professional bodies have recommended discontinuing fertility services during the pandemic such that reproductive services have also been affected. Although increased safety measures have helped to mitigate the propagation of COVID-19 in a number of countries, it seems that there is no predictable timeline to containment of the virus, a goal likely to remain elusive until an effective vaccine becomes available  and widely distributed across the globe. In parallel, research on reproduction has been postponed for obvious reasons, while diagnostic tests that detect the virus or antibodies against it are of vital importance to support public health policies, such as social distancing and our obligation to wear masks in public spaces. This review aims to provide an overview of critical research and ethics issues that have been continuously emerging in the field of reproductive medicine as the COVID-19 pandemic tragically unfolds.Abbreviations: ACE2: angiotensin- converting enzyme 2; ART: Assisted reproductive technology; ASRM: American Society for Reproductive Medicine; CCR9: C-C Motif Chemokine Receptor 9; CDC: Centers for Disease Control and Prevention; COVID-19: Coronavirus disease 2019; Ct: Cycle threshold; CXCR6: C-X-C Motif Chemokine Receptor 6; ELISA: enzyme-linked immunosorbent assay; ESHRE: European Society of Human Reproduction and Embryology; ET: Embryo transfer; FSH: Follicle Stimulating Hormone; FFPE: formalin fixed paraffin embedded; FYCO1: FYVE And Coiled-Coil Domain Autophagy Adaptor 1; IFFS: International Federation of Fertility Societies; IUI: Intrauterine insemination; IVF: In vitro fertilization; LH: Luteinizing Hormone; LZTFL1: Leucine Zipper Transcription Factor Like 1; MAR: medically assisted reproduction services; MERS: Middle East Respiratory syndrome; NGS: Next Generation Sequencing; ORF: Open Reading Frame; PPE: personal protective equipment; RE: RNA Element; REDa: RNA Element Discovery algorithm; RT-PCR: Reverse=trascriptase transcriptase-polymerase chain reaction; SARS: Severe acute respiratory syndrome; SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2; SLC6A20: Solute Carrier Family 6 Member 20; SMS: Single Molecule Sequencing; T: Testosterone; TMPRSS2: transmembrane serine protease 2; WHO: World Health Organization; XCR1: X-C Motif Chemokine Receptor.

Comorbidities' potential impacts on severe and non-severe patients with COVID-19: A systematic review and meta-analysis

BACKGROUND

An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus (SARS-CoV-2) emerged in December 2019 in Wuhan, China. Epidemiologic evidence suggests that patients with comorbidities and novel coronavirus disease 2019 (COVID-19) infection may have poor survival outcomes. However, the risk of these coexisting medical conditions in severe and non-severe cases has not been systematically reported.

PURPOSE

The present study aimed to estimate the association of chronic comorbidities in severe and non-severe cases.

METHODS

A literature search was conducted using the databases PubMed, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Database, Chinese Scientific Journals Full-text Database (CQVIP) from the inception dates to April 1, 2020, to identify cohort studies assessing comorbidity and risk of adverse outcome. Either a fixed- or random-effects model was used to calculate the overall combined risk estimates.

RESULTS

A total of 22 studies involving 3286 patients with laboratory-confirmed COVID-19 were included in the analysis. Overall, compared with the patients with non-severe cases, the pooled odds ratios (ORs) of hypertension, diabetes mellitus, and cardiovascular, cerebrovascular, and respiratory diseases in patients with severe cases were 2.79 (95% confidence intervals [95% CI]: 1.66-4.69), 1.64 (95% CI: 2.30-1.08), 1.79 (95% CI: 1.08-2.96), 3.92 (95% CI: 2.45-6.28), and 1.98 (95% CI: 1.26-3.12), respectively.

CONCLUSIONS

This meta-analysis supports the finding that chronic comorbidities may contribute to severe outcome in patients with COVID-19. According to the findings of the present study, old age and 2 or more comorbidities are significantly impactful to COVID-19 outcomes in hospitalized patients in China.

Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients

The pandemic of coronavirus disease 2019 (COVID-19) urgently calls for more sensitive molecular diagnosis to improve sensitivity of current viral nuclear acid detection. We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and implementing AP dually targeting the N gene of SARS-CoV-2 RNA and RNase 1, 3, 6. The arbitrarily primed polymerase chain reaction (AP-PCR) improvement of viral RNA integrity was supported by (a) the AP increased resistance of the targeted gene (N gene) of SARS-CoV-2 RNA to RNase treatment; (b) the detection of SARS-CoV-2 RNA by AP-PCR with lower cycle threshold values (-2.7 cycles) compared to two commercially available assays; (c) improvement of the viral RNA stability of the ORF gene upon targeting of the N gene and RNase. Furthermore, the improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70-80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases. Lastly, AP-PCR analysis of 306 confirmed and convalescent cases revealed prolonged presence of viral loading for >20 days after the first positive diagnosis. Thus, the AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.

Functional profiling of COVID-19 respiratory tract microbiomes

In response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.

Red Cell Distribution Width Upon Hospital Admission Predicts Short-Term Mortality in Hospitalized Patients With COVID-19: A Single-Center Experience

Background: Coronavirus disease (COVID-19) was first described at the end of 2019 in China and has since spread across the globe. Red cell distribution width (RDW) is a potent prognostic marker in several medical conditions and has recently been suggested to be of prognostic value in COVID-19.

Methods: This retrospective, observational study of consecutive patients with COVID-19 was conducted from March 12, 2020 to December 4, 2020 in the Wilhelminenhospital, Vienna, Austria. RDWlevels on admission were collected and tested for their predictive value of 28-day mortality.

Results: A total of 423 eligible patients with COVID-19 were included in the final analyses and 15.4% died within 28 days (n = 65). Median levels of RDWwere significantly higher in non-survivors compared to survivors [14.6% (IQR, 13.7–16.3) vs. 13.4% (IQR, 12.7– 14.4), P < 0.001]. Increased RDW was a significant predictor of 28-day mortality [crude odds ratio (OR) 1.717, 95% confidence interval (CI) 1.462–2.017; P = < 0.001], independent of clinical confounders, comorbidities and established prognostic markers of COVID-19 (adjusted OR of the final model 1.368, 95% CI 1.126–1.662; P = 0.002). This association remained consistent upon sub-group analysis. Our study data also demonstrate that RDW levels upon admission for COVID-19 were similar to previously recorded, non-COVID-19 associated RDW levels [14.2% (IQR, 13.3–15.7) vs. 14.0% [IQR, 13.2–15.1]; P = 0.187].

Conclusions: In this population, RDWwas a significant, independent prognostic marker of short-term mortality in patients with COVID-19.

Spiking dependence of SARS-CoV-2 pathogenicity on TMPRSS2

Epidemiological data shows a discrepancy in COVID‐19 susceptibility and outcomes with some regions being more heavily affected than others. However, the factors that determine host susceptibility and pathogenicity remain elusive. An increasing number of publications highlight the role of Transmembrane Serine Protease 2 (TMPRSS2) in the susceptibility of the host cell to SARS‐CoV‐2. Cleavage of viral spike protein via the host cell's TMPRSS2 enzyme activity mediates viral entry into the host cell. The enzyme synthesis is regulated by the TMPRSS2 gene, which has also been implicated in the entry mechanisms of previously reported Coronavirus infections. In this review, we have investigated the pathogenicity of SARS‐CoV‐2 and disease susceptibility dependence on the TMPRSS2 gene as expressed in various population groups. We further discuss how the differential expression of this gene in various ethnic groups can affect the SARS‐CoV‐2 infection and Coronavirus disease (COVID)‐19 outcomes. Moreover, promising new TMPRSS2 protease blockers and inhibitors are discussed for COVID‐19 treatment.

1. Entry of SARS‐CoV‐2 into a host cell depends on host protease TMPRSS2.

2. TMPRSS2 gene has localized expression throughout the human body but highly expressed in cells of the respiratory tract (primary target of SARS‐CoV‐2 in humans), gastrointestinal tract, kidneys and prostate.

3. Differences in expression of TMPRSS2 gene in the respiratory among different population groups can be a basis for discrepancy observed in COVID‐19 susceptibility and disease outcomes.

4. Drugs based on the inhibition or blockage of TMPRSS2 protease are undergoing clinical trials as a therapeutic option.

Indoor Model Simulation for COVID-19 Transport and Exposure

Transmission of respiratory viruses is a complex process involving emission, deposition in the airways, and infection. Inhalation is often the most relevant transmission mode in indoor environments. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the risk of inhalation transmission is not yet fully understood. Here, we used an indoor aerosol model combined with a regional inhaled deposited dose model to examine the indoor transport of aerosols from an infected person with novel coronavirus disease (COVID-19) to a susceptible person and assess the potential inhaled dose rate of particles. Two scenarios with different ventilation rates were compared, as well as adult female versus male recipients. Assuming a source strength of 10 viruses/s, in a tightly closed room with poor ventilation (0.5 h-1), the respiratory tract deposited dose rate was 140-350 and 100-260 inhaled viruses/hour for males and females; respectively. With ventilation at 3 h-1 the dose rate was only 30-90 viruses/hour. Correcting for the half-life of SARS-CoV-2 in air, these numbers are reduced by a factor of 1.2-2.2 for poorly ventilated rooms and 1.1-1.4 for well-ventilated rooms. Combined with future determinations of virus emission rates, the size distribution of aerosols containing the virus, and the infectious dose, these results could play an important role in understanding the full picture of potential inhalation transmission in indoor environments.

Food Safety in Post-COVID-19 Pandemic: Challenges and Countermeasures

Understanding food safety hazard risks is essential to avoid potential negative heath impacts in the food supply chain in a post-COVID-19 pandemic era. Development of strategies for virus direction in foods plays an important role in food safety and verification. Early warning, tracing, and detection should be implemented as an integrated system in order to mitigate thecoronavirus disease 2019 (COVID-19) outbreak, in which the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical as it not only concerns screening of populations but also monitoring of possible contaminated sources such as the food supply chain. In this review, we point out the consequences in different aspects of our daily life in the post-COVID-19 pandemic from the perspective of the food supply chain and the food industry. We summarize the possible transmission routes of COVID-19 in the food supply chain before exploring the development of corresponding detection tools of SARS-CoV-2. Accordingly, we compare different detection methods for the virus in foods, including different pretreatments of food matrices in the virus detection. Finally, the future perspectives are proposed.

Immunotoxic role of organophosphates: An unseen risk escalating SARS-CoV-2 pathogenicity

Consistent gathering of immunotoxic substances on earth is a serious global issue affecting people under pathogenic stress. Organophosphates are among such hazardous compounds that are ubiquitous in nature. They fuel oxidative stress to impair antiviral immune response in living entities. Aside, organophosphates promote cytokine burst and pyroptosis in broncho-alveolar chambers leading to severe respiratory ailments. At present, we witness COVID-19 outbreak caused by SARS-CoV-2. Infection triggers cytokine storm coupled with inflammatory manifestations and pulmonary disorders in patients. Since organophosphate-exposure promotes necroinflammation and respiratory troubles hence during current pandemic situation, additional exposure to such chemicals can exacerbate inflammatory outcome and pulmonary maladies in patients, or pre-exposure to organophosphates might turn-out to be a risk factor for compromised immunity. Fortunately, antioxidants alleviate organophosphate-induced immunosuppression and hence under co-exposure circumstances, dietary intake of antioxidants would be beneficial to boost immunity against SARS-CoV-2 infection.

The genetic structure of SARS-CoV-2 does not rule out a laboratory origin: SARS-COV-2 chimeric structure and furin cleavage site might be the result of genetic manipulation

Severe acute respiratory syndrome-coronavirus (SARS-CoV)-2's origin is still controversial. Genomic analyses show SARS-CoV-2 likely to be chimeric, most of its sequence closest to bat CoV RaTG13, whereas its receptor binding domain (RBD) is almost identical to that of a pangolin CoV. Chimeric viruses can arise via natural recombination or human intervention. The furin cleavage site in the spike protein of SARS-CoV-2 confers to the virus the ability to cross species and tissue barriers, but was previously unseen in other SARS-like CoVs. Might genetic manipulations have been performed in order to evaluate pangolins as possible intermediate hosts for bat-derived CoVs that were originally unable to bind to human receptors? Both cleavage site and specific RBD could result from site-directed mutagenesis, a procedure that does not leave a trace. Considering the devastating impact of SARS-CoV-2 and importance of preventing future pandemics, researchers have a responsibility to carry out a thorough analysis of all possible SARS-CoV-2 origins.

SARS-CoV-2: what it is, how it acts, and how it manifests in imaging studies

COVID-19 is a disease with many clinical, biochemical, and radiological signs that has a predilection for the lungs, probably because of the high number of ACE-2 receptors in this organ. The infection of cells activates proinflammatory substances, causing diffuse alveolar damage, which is the histopathological basis of ARDS. The exudative phase would manifest as ground-glass opacities and consolidation, and the proliferative phase would manifest as a tendency toward a more linear morphology. Both CT and PET/CT findings support the inflammatory character of the lung lesions in the initial phase of the disease and in patients with mild-moderate disease. Severe cases have pulmonary hypoperfusion that is likely due to abnormal alveolar ventilation and perfusion. On the other hand, a prothrombotic state increases the risk of thromboembolic disease through the activation of coagulation and platelet pathways with the production of fibrin degradation products (D-dimer) and consumption of platelets.

SARS-CoV-2: what it is, how it acts, and how it manifests in imaging studies

COVID-19 is a disease with many clinical, biochemical, and radiological signs that has a predilection for the lungs, probably because of the high number of ACE-2 receptors in this organ. The infection of cells activates proinflammatory substances, causing diffuse alveolar damage, which is the histopathological basis of ARDS. The exudative phase would manifest as ground-glass opacities and consolidation, and the proliferative phase would manifest as a tendency toward a more linear morphology. Both CT and PET/CT findings support the inflammatory character of the lung lesions in the initial phase of the disease and in patients with mild-moderate disease.

Severe cases have pulmonary hypoperfusion that is likely due to abnormal alveolar ventilation and perfusion. On the other hand, a prothrombotic state increases the risk of thromboembolic disease through the activation of coagulation and platelet pathways with the production of fibrin degradation products (D-dimer) and consumption of platelets.

Quantitative assessment of SARS-CoV-2 RNAemia and outcome in patients with coronavirus disease 2019

The disease spectrum of coronavirus disease 2019 (COVID‐19) varies from asymptomatic infection to critical illness and death. Identification of prognostic markers is vital for predicting progression and clinical practice. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA, known as RNAemia, has been detected in the blood. However, the potential clinical value of SARS‐CoV‐2 RNAemia remains unknown. We, therefore, conducted a meta‐analysis using a random‐effects model to estimate the pooled prevalence of SARS‐CoV‐2 RNAemia as well as summary strength of RNAemia in association with disease severity and unfavorable clinical outcomes. A total of 21 studies involving 2181 patients were included. SARS‐CoV‐2 RNAemia in COVID‐19 patients varied from 9.4% to 74.1%, with a pooled estimate of 34% (95% confidene interval [CI]: 26%–43%). Overall, SARS‐CoV‐2 RNAemia was associated with COVID‐19 severity with odds ratio (OR) of 5.43 (95% CI: 3.46–8.53). In addition, SARS‐CoV‐2 RNAemia was a significant risk factor for unfavorable clinical outcomes (OR = 6.54, 95% CI: 3.82–11.21). The summary OR was 4.28 (95% CI: 2.20–8.33) for intensive care unit (ICU) admission, 11.07 (95% CI: 5.60–21.88) for mortality. Furthermore, RNAemia was also a significant risk factor for invasive mechanical ventilation and multiple organ failure. SARS‐CoV‐2 RNAemia is associated with disease severity, ICU admission, death in COVID‐19, and may serve as a clinical predictor. More prospective trials in evaluating the potential of SARS‐CoV‐2 RNAemia as a prognostic indicator are necessary.

SARS-CoV-2 Infection and Disease Modelling Using Stem Cell Technology and Organoids

In this Review, we briefly describe the basic virology and pathogenesis of SARS-CoV-2, highlighting how stem cell technology and organoids can contribute to the understanding of SARS-CoV-2 cell tropisms and the mechanism of disease in the human host, supporting and clarifying findings from clinical studies in infected individuals. We summarize here the results of studies, which used these technologies to investigate SARS-CoV-2 pathogenesis in different organs. Studies with in vitro models of lung epithelia showed that alveolar epithelial type II cells, but not differentiated lung alveolar epithelial type I cells, are key targets of SARS-CoV-2, which triggers cell apoptosis and inflammation, while impairing surfactant production. Experiments with human small intestinal organoids and colonic organoids showed that the gastrointestinal tract is another relevant target for SARS-CoV-2. The virus can infect and replicate in enterocytes and cholangiocytes, inducing cell damage and inflammation. Direct viral damage was also demonstrated in in vitro models of human cardiomyocytes and choroid plexus epithelial cells. At variance, endothelial cells and neurons are poorly susceptible to viral infection, thus supporting the hypothesis that neurological symptoms and vascular damage result from the indirect effects of systemic inflammatory and immunological hyper-responses to SARS-CoV-2 infection.

Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

Rapid and sensitive triple-mode detection of causative SARS-CoV-2 virus specific genes through interaction between genes and nanoparticles

The recent outbreak of coronavirus disease 2019 (COVID-19) is highly infectious, which threatens human health and has received increasing attention. So far, there is no specific drug or vaccine for COVID-19. Therefore, it is urgent to establish a rapid and sensitive early diagnosis platform, which is of great significance for physical separation of infected persons after rapid diagnosis. Here, we propose a colorimetric/SERS/fluorescence triple-mode biosensor based on AuNPs for the fast selective detection of viral RNA in 40 min. AuNPs with average size of 17 nm were synthesized, and colorimetric, surface enhanced Raman scattering (SERS), and fluorescence signals of sensors are simultaneously detected based on their basic aggregation property and affinity energy to different bio-molecules. The sensor achieves a limit detection of femtomole level in all triple modes, which is 160 fM in absorbance mode, 259 fM in fluorescence mode, and 395 fM in SERS mode. The triple-mode signals of the sensor are verified with each other to make the experimental results more accurate, and the capacity to recognize single-base mismatch in each working mode minimizes the false negative/positive reading of SARS-CoV-2. The proposed sensing platform provides a new way for the fast, sensitive, and selective detection of COVID-19 and other diseases.

Nanomaterials to tackle the COVID-19 pandemic

The rapid worldwide spread of the COVID-19 pandemic, caused by the severe acute respiratory SARS-CoV-2, has created an urgent need for its diagnosis and treatment. As a result, many researchers have sought to find the most efficient and appropriate methods to detect and treat the SARS-CoV-2 virus over the past few months. Real-time reverse-transcriptase polymerase chain reaction (RT-PCR) testing is currently used as one of the most reliable methods to detect the new virus; however, this method is time-consuming, labor-intensive, and requires trained laboratory workers. Moreover, despite its high sensitivity and specificity, false negatives are reported, especially in non-nasopharyngeal swab samples that yield lower viral loads. Therefore, designing and employing faster and more reliable methods seems necessary. In recent years, many attempts have been made to fabricate various nanomaterial-based biosensors to detect viruses and bacteria in clinical samples. The use of nanomaterials plays a significant role in improving the performance of biosensors. Plasmonic biosensors, field-effect transistor (FET)-based biosensors, electrochemical biosensors, and reverse transcription loop-mediated isothermal amplification (RT-LAMP) methods are only some of the effective ways to detect viruses. However, to use these biosensors to detect the SARS-CoV-2 virus, modifications must be performed to increase sensitivity and speed of testing due to the rapidly spreading nature of SARS-CoV-2, which requires an early point of care detection and treatment for pandemic control. Several studies have been carried out to show the nanomaterial-based biosensors' performance and success in detecting the novel virus. The limit of detection, accuracy, selectivity, and detection speed are some vital features that should be considered during the design of the SARS-CoV-2 biosensors. This review summarizes various nanomaterials-based sensor platforms to detect the SARS-CoV-2, and their design, advantages, and limitations.

Immunopathological Changes in SARS-CoV-2 Critical and Non-critical Pneumonia Patients: A Systematic Review to Determine the Cause of Co-infection

The ongoing COVID-19 pandemic originating from Wuhan, China is causing major fatalities across the world. Viral pneumonia is commonly observed in COVID-19 pandemic. The number of deaths caused by viral pneumonia is mainly due to secondary bacterial or fungal infection. The immunopathology of SARS-CoV-2 viral pneumonia is poorly understood with reference to human clinical data collected from patients infected by virus and secondary bacterial or fungal infection occurring simultaneously. The co-infection inside the lungs caused by pneumonia has direct impact on the changing lymphocyte and neutrophil counts. Understanding the attribution of these two immunological cells triggered by cytokines level change is of great importance to identify the progression of pneumonia from non-severe to severe state in hospitalized patients. This review elaborates the cytokines imbalance observed in SARS-CoV-1 (2003 epidemic), SARS-CoV-2 (2019 pandemic) viral pneumonia and community acquired pneumonia (CAP), respectively, in patients to determine the potential reason of co-infection. In this review the epidemiology, virology, clinical symptoms, and immunopathology of SARS-CoV-2 pneumonia are narrated. The immune activation during SARS-CoV-1 pneumonia, bacterial, and fungal pneumonia is discussed. Here it is further analyzed with the available literatures to predict the potential internal medicines, prognosis and monitoring suggesting better treatment strategy for SARS-CoV-2 pneumonia patients.

Nebuliser Type Influences Both Patient-Derived Bioaerosol Emissions and Ventilation Parameters during Mechanical Ventilation

COVID-19 may lead to serious respiratory complications which may necessitate ventilatory support. There is concern surrounding potential release of patient-derived bioaerosol during nebuliser drug refill, which could impact the health of caregivers. Consequently, mesh nebulisers have been recommended by various clinical practice guidelines. Currently, there is a lack of empirical data describing the potential for release of patient-derived bioaerosol during drug refill. This study examined the release of simulated patient-derived bioaerosol, and the effect on positive end expiratory pressure during nebuliser refill during mechanical ventilation of a simulated patient. During jet nebuliser refill, the positive end expiratory pressure decreased from 4.5 to 0 cm H2O. No loss in pressure was noted during vibrating mesh nebuliser refill. A median particle number concentration of 710 particles cm-3 above ambient was detected when refilling the jet nebuliser in comparison to no increase above ambient detected when using the vibrating mesh nebuliser. The jet nebuliser with the endotracheal tube clamped resulted in 60 particles cm-3 above ambient levels. This study confirms that choice of nebuliser impacts both the potential for patient-derived bioaerosol release and the ability to maintain ventilator circuit pressures and validates the recommended use of mesh nebulisers during mechanical ventilation.

COVID-19 Pandemic and Its Impact on Pediatric Dentistry in Austria: Knowledge, Perception and Attitude Among Pediatric Dentists in a Cross-Sectional Survey

Introduction

The Novel Coronavirus Disease (COVID-19) outbreak is affecting people worldwide. Given the frequent production of aerosols, dentists are a high-risk group for infection. The aim of this study was to assess the knowledge, perception and attitude regarding COVID-19 among pediatric dentists in Austria.

Methods

An online survey was distributed among the 128 pediatric dentists that are members of the Austrian Society of Pediatric Dentistry. The questionnaire was divided into three sections: 1) dentists’ demographic characteristics, 2) general knowledge and attitude, 3) COVID-19 with a focus on pediatric dentistry.

Results

Seventy-five dentists replied; 58 questionnaires could be included in the analysis (93.1% female). Pediatric dentists were found to have good general knowledge of COVID-19. However, only 10% had attended training or lectures and 36.2% rated their role in teaching patients about COVID-19 as being very significant. At the beginning of the outbreak, 78.6% only offered emergency services. Currently, only 10.3% of the dentists work without FFP2/3 mask when producing aerosols.

Discussion

Austrian pediatric dentists were aware of the general aspects of COVID-19. Those, who had their practice open mostly followed national and international recommendations given and only offered emergency visits.

A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests

The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. A reference standard with a well-characterized concentration or titer is of the utmost importance for the study of limit of detection (LoD), which is a crucial feature for a diagnostic assay. Although several reference standards of plasmids or synthetic RNA have already been announced, a reference standard for inactivated virus particles with an accurate concentration is still needed to evaluate the complete procedure. Here, we performed a collaborative study to estimate the NAT-detectable units as a viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6 × 105 ± 6.5 × 104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.

Supplementation with vitamin D in the COVID-19 pandemic?

The coronavirus disease 2019 (COVID-19) pandemic was declared a public health emergency of international concern by the World Health Organization. COVID-19 has high transmissibility and could result in acute lung injury in a fraction of patients. By counterbalancing the activity of the renin-angiotensin system, angiotensin-converting enzyme 2, which is the fusion receptor of the virus, plays a protective role against the development of complications of this viral infection. Vitamin D can induce the expression of angiotensin-converting enzyme 2 and regulate the immune system through different mechanisms. Epidemiologic studies of the relationship between vitamin D and various respiratory infections were reviewed and, here, the postulated mechanisms and clinical data supporting the protective role of vitamin D against COVID-19-mediated complications are discussed.

An Overview of Nucleic Acid Testing for the Novel Coronavirus SARS-CoV-2

In this note we analyze the problems in the nucleic acid testing (NAT) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we also give some suggestions for improving the accuracy of NAT diagnosis. NAT testing is considered to be the diagnostic “gold standard”; at present there are few reviews on NAT for SARS-CoV-2. Moreover, many false-negative results always appear in the procedure of detecting, which has affected early diagnosis of the disease and brought a great challenge to mitigation and containment of the pandemic. In conclusion, comprehensive analyses of serological and imaging findings should be performed to guide the formulation of an accurate clinical diagnosis, treatment plan, and monitoring therapeutic efficacy, in an effort to achieve early diagnosis, containment, and treatment of the disease, thereby effectively reducing progression of the pandemic. This article presents a literature overview of SARS-CoV-2 nucleic acid testing, aiming to provide support for clinicians.

Texture Analysis in the Evaluation of Covid-19 Pneumonia in Chest X-Ray Images: a Proof of Concept Study

BACKGROUND

One of the most challenging aspects related to Covid-19 is to establish the presence of infection in early phase of the disease. Texture analysis might be an additional tool for the evaluation of Chest X-ray in patients with clinical suspicion of Covid-19 related pneumonia.

OBJECTIVE

To evaluate the diagnostic performance of texture analysis and machine learning models for the diagnosis of Covid-19 interstitial pneumonia in Chest X-ray images.

METHODS

Chest X-ray images were accessed from a publicly available repository (https://www.kaggle.com/tawsifurrahman/covid19-radiography-database). Lung areas were manually segmented using a polygonal regions of interest covering both lung areas, using MaZda, a freely available software for texture analysis. A total of 308 features per ROI was extracted. One hundred-ten Covid-19 Chest X-ray images were selected for the final analysis.

RESULTS

Six models, namely NB, GLM, DL, GBT, ANN and PLS-DA were selected and ensembled. According to Youden's index, the Covid-19 Ensemble Machine Learning Score showing the highest Area Under the Curve (0.971±0.015) was 132.57. Assuming this cut-off the Ensemble model performance was estimated evaluating both true and false positive/negative, resulting in 91.8% accuracy with 93% sensitivity and 90% specificity. Moving the cut-off value to -100, although the accuracy resulted lower (90.6%), the Ensemble Machine Learning showed 100% sensitivity, with 80% specificity.

CONCLUSION

Texture analysis of Chest X-ray images and machine learning algorithms may help in differentiating patients with Covid-19 pneumonia. Despite several limitations, this study can lay ground for future researches in this field and help developing more rapid and accurate screening tools for these patients.

Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea

We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.

High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.

Advances in emergent biological recognition elements and bioelectronics for diagnosing COVID-19

Coronaviruses pose a serious threat to public health. Tremendous efforts are dedicated to advance reliable and effective detection of coronaviruses. Currently, the coronavirus disease 2019 (COVID-19) diagnosis mainly relies on the detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic materials by using reverse transcription-polymerase chain reaction (RT-PCR) assay. However, simpler and more rapid and reliable alternatives are needed to meet high demand during the pandemic. Biosensor-based diagnosis approaches become alternatives for selectively and rapidly detecting virus particles because of their biorecognition elements consisting of biomaterials that are specific to virus biomarkers. Here, we summarize biorecognition materials, including antibodies and antibody-like molecules, that are designed to recognize SARS-CoV-2 biomarkers and the advances of recently developed biosensors for COVID-19 diagnosis. The design of biorecognition materials or layers is crucial to maximize biosensing performances, such as high selectivity and sensitivity of virus detection. Additionally, the recent representative achievements in developing bioelectronics for sensing coronavirus are included. This review includes scholarly articles, mainly published in 2020 and early 2021. In addition to capturing the fast development in the fields of applied materials and biodiagnosis, the outlook of this rapidly evolving technology is summarized. Early diagnosis of COVID-19 could help prevent the spread of this contagious disease and provide significant information to medical teams to treat patients.

Clinical characteristics and analysis of risk factors for disease progression of COVID-19: A retrospective Cohort Study

Objective: Since December 2019, an outbreak of coronavirus disease 2019 (COVID 19) has been experienced from Wuhan, China to the world. A retrospective cohort study was conducted to summarize the clinical characteristics of patients with COVID-19 and to explore the risk factors affecting the disease duration in Jiangan Fangcang shelter hospital, Wuhan, China. Methods: Clinical characteristics of 409 patients with COVID-19 were retrospectively analyzed. We describe the clinical characteristics and distribution of discharge time or transfer time for each patient. Then we performed univariate and multivariate Cox regression analysis to identify potential risk factors for progression from non-severe to severe COVID-19 or death. Results: The median disease duration of all patients was 23 days (IQR 19-28). The main symptoms of the patient were fever (95.6%), cough (74.3%), tiredness (21.5%), and so on. Comorbidities mainly included hypertension (30.6%) diabetes (17.6%) and heart disease (12.5%). The univariate Cox regression analysis showed that old age, number of symptoms, the combination of hypertension, heart disease and pulmonary disease were associated with the progression of disease. The multivariate Cox regression analysis showed that old age (HR: 7.294; 95% CI: 1.442-36.888; P = 0.016), the combination of hypertension (HR: 2.230; 95% CI: 1.090-4.562; P = 0.028) and heart disease (HR: 2.650; 95% CI: 1.079-6.510; P = 0.034) were independent risk factors for progression of COVID-19. Conclusions: The age of the patient, the combination of hypertension and heart disease were independent risk factors for the progression of COVID-19. Cautions should be raised for patients with these risk factors.

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.

Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review

BACKGROUND

The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic.

METHODS

We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose.

RESULTS

From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic.

CONCLUSION

We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.

SARS-CoV-2 (COVID-19): Beginning to Understand a New Virus

Within the last two decades, several members of the Coronaviridae family demonstrated epidemic potential. In late 2019, an unnamed genetic relative, later named SARS-CoV-2 (COVID-19), erupted in the highly populous neighborhoods of Wuhan, China. Unchecked, COVID-19 spread rapidly among interconnected communities and related households before containment measures could be enacted. At present, the mortality rate of COVID-19 infection worldwide is 6.6%. In order to mitigate the number of infections, restrictions or recommendations on the number of people that can gather in a given area have been employed by governments worldwide. For governments to confidently lift these restrictions as well as counter a potential secondary wave of infections, alternative medications and diagnostic strategies against COVID-19 are urgently required. This review has focused on these issues.

Review of analytical performance of COVID-19 detection methods

In the recent SARS-CoV-2 pandemic, public health experts have emphasized testing, tracking infected people, and tracing their contacts as an effective strategy to reduce the spread of the virus. Several diagnostic methods are reported for detecting the coronavirus in clinical, research, and public health laboratories. Some tests detect the infection directly by detecting the viral RNA and other tests detect the infection indirectly by detecting the host antibodies. A diagnostic test during the pandemic should help make an appropriate clinical decision in a short period of time. Recently reported diagnostic methods for SARS-CoV-2 have varying throughput, batching capacity, requirement of infrastructure setting, analytical performance, and turnaround times ranging from a few minutes to several hours. These factors should be considered while selecting a reliable and rapid diagnostic method to help make an appropriate decision and prompt public health interventions. This paper reviews recent SARS-CoV-2 diagnostic methods published in journals and reports released by regulatory agencies. We compared the analytical efficiency including limit of detection, sensitivity, specificity, and throughput. In addition, we also looked into ease of use, affordability, and availability of accessories. Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.

Prevalence and risk factors of disability and anxiety in a retrospective cohort of 432 survivors of Coronavirus Disease-2019 (Covid-19) from China

OBJECTIVE

To estimate the prevalence of disability and anxiety in Covid-19 survivors at discharge from hospital and analyze relative risk by exposures.

DESIGN

Multi-center retrospective cohort study.

SETTING

Twenty-eight hospitals located in eight provinces of China.

METHODS

A total of 432 survivors with laboratory-confirmed SARS CoV-2 infection participated in this study. At discharge, we assessed instrumental activities of daily living (IADL) with Lawton's IADL scale, dependence in activities of daily living (ADL) with the Barthel Index, and anxiety with Zung's self-reported anxiety scale. Exposures included comorbidity, smoking, setting (Hubei vs. others), disease severity, symptoms, and length of hospital stay. Other risk factors considered were age, gender, and ethnicity (Han vs. Tibetan).

RESULTS

Prevalence of at least one IADL problem was 36.81% (95% CI: 32.39-41.46). ADL dependence was present in 16.44% (95% CI: 13.23-20.23) and 28.70% (95% CI: 24.63-33.15) were screened positive for clinical anxiety. Adjusted risk ratio (RR) of IADL limitations (RR 2.48, 95% CI: 1.80-3.40), ADL dependence (RR 2.07, 95% CI 1.15-3.76), and probable clinical anxiety (RR 2.53, 95% CI 1.69-3.79) were consistently elevated in survivors with severe Covid-19. Age was an additional independent risk factor for IADL limitations and ADL dependence; and setting (Hubei) for IADL limitations and anxiety. Tibetan ethnicity was a protective factor for anxiety but a risk factor for IADL limitations.

CONCLUSION

A significant proportion of Covid-19 survivors had disability and anxiety at discharge from hospital. Health systems need to be prepared for an additional burden resulting from rehabilitation needs of Covid-19 survivors.

Essential interpretations of bioinformatics in COVID-19 pandemic

The currently emerging pathogen SARS-CoV-2 has produced the global pandemic crisis by causing COVID-19. The unique and novel genetic makeup of SARS-CoV-2 has created hurdles in biological research, due to which the potential drug/vaccine candidates have not yet been discovered by the scientific community. Meanwhile, the advantages of bioinformatics in viral research had created a milestone since last few decades. The exploitation of bioinformatics tools and techniques has successfully interpreted this viral genomics architecture. Some major in silico studies involving next-generation sequencing, genome-wide association studies, computer-aided drug design etc. have been effectively applied in COVID-19 research methodologies and discovered novel information on SARS-CoV-2 in several ways. Nowadays the implementation of in silico studies in COVID-19 research has not only sequenced the SARS-CoV-2 genome but also properly analyzed the sequencing errors, evolutionary relationship, genetic variations, putative drug candidates against SARS-CoV-2 viral genes etc. within a very short time period. These would be very needful towards further research on COVID-19 pandemic and essential for vaccine development against SARS-CoV-2 which will save public health.

Mesenchymal stromal cells to fight SARS-CoV-2: Taking advantage of a pleiotropic therapy

The devastating global impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has prompted scientists to develop novel strategies to fight Coronavirus Disease of 2019 (COVID-19), including the examination of pre-existing treatments for other viral infections in COVID-19 patients. This review provides a reasoned discussion of the possible use of Mesenchymal Stromal Cells (MSC) or their products as a treatment in SARS-CoV-2-infected patients. The main benefits and concerns of using this cellular therapy, guided by preclinical and clinical data obtained from similar pathologies will be reviewed. MSC represent a highly immunomodulatory cell population and their use may be safe according to clinical studies developed in other pathologies. Notably, four clinical trials and four case reports that have already been performed in COVID-19 patients obtained promising results. The clinical application of MSC in COVID-19 is very preliminary and further investigational studies are required to determine the efficacy of the MSC therapy. Nevertheless, these preliminary studies were important to understand the therapeutic potential of MSC in COVID-19. Based on these encouraging results, the United States Food and Drug Administration (FDA) authorized the compassionate use of MSC, but only in patients with Acute Respiratory Distress Syndrome (ARDS) and a poor prognosis. In fact, patients with severe SARS-CoV-2 can present infection and tissue damage in different organs, such as lung, heart, liver, kidney, gut and brain, affecting their function. MSC may have pleiotropic activities in COVID-19, with the capacity to fight inflammation and repair lesions in several organs.

Facile biosensors for rapid detection of COVID-19

Currently the world is being challenged by a public health emergency caused by the coronavirus pandemic (COVID-19). Extensive efforts in testing for coronavirus infection, combined with isolating infected cases and quarantining those in contact, have proven successful in bringing the epidemic under control. Rapid and facile screening of this disease is in high demand. This review summarises recent advances in strategies reported by international researchers and engineers concerning how to tackle COVID-19 via rapid testing, mainly through nucleic acid- and antibody- testing. The roles of biosensors as powerful analytical tools are emphasized for the detection of viral RNAs, surface antigens, whole viral particles, antibodies and other potential biomarkers in human specimen. We critically review in depth newly developed biosensing methods especially for in-field and point-of-care detection of SARS-CoV-2. Additionally, this review describes possible future strategies for virus rapid detection. It helps researchers working on novel sensor technologies to tailor their technologies in a way to address the challenge for effective detection of COVID-19.

A high-throughput drug screening strategy against coronaviruses

The emergence and re-emergence of coronaviruses (CoV) continually cause circulating epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. The resultant disease, coronavirus disease 2019 (COVID-19), has rapidly developed into a worldwide pandemic, leading to severe health and economic burdens. Although the recently announced vaccines against COVID-19 has rekindled hope, there is still a major challenge to urgently meet the global need for rapid treatment of the pandemic. Given the urgency of the CoV outbreak, we propose a strategy to screen potential broad-spectrum drugs against CoV in a high-throughput manner, particularly against SARS-CoV-2. Since the essential functional domains of CoV are extensively homologous, the availability of two types of mild CoV, HCoV-OC43 and MHV, should provide a valuable tool for the rapid identification of promising drugs against CoV without the drawbacks of level three biological confinements. The luciferase reporter gene is introduced into HCoV-OC43 and MHV to indicate viral activity, and hence the antiviral efficiency of screened drugs can be quantified by luciferase activity. Compounds with antiviral activity against both HCoV-OC43 and MHV are further evaluated in SARS-CoV-2 after structural optimizations. This system allows large-scale compounds to be screened to search for broad-spectrum drugs against CoV in a high-throughput manner, providing potential alternatives for clinical management of SARS-CoV-2 or other CoV.

Long-term ACE Inhibitor/ARB Use Is Associated With Severe Renal Dysfunction and Acute Kidney Injury in Patients With Severe COVID-19: Results From a Referral Center Cohort in the Northeast of France

Background

In patients with severe coronavirus disease 2019 (COVID-19), data are scarce and conflicting regarding whether chronic use of angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) influences disease outcomes. In patients with severe COVID-19, we assessed the association between chronic ACEI/ARB use and the occurrence of kidney, lung, heart, and liver dysfunctions and the severity of the inflammatory reaction as evaluated by biomarkers kinetics, and their association with disease outcomes.

Methods

We performed a retrospective longitudinal cohort study on consecutive patients with newly diagnosed severe COVID-19. Independent predictors were assessed through receiver operating characteristic analysis, time-series analysis, logistic regression analysis, and multilevel modeling for repeated measures.

Results

On the 149 patients included in the study 30% (44/149) were treated with ACEI/ARB. ACEI/ARB use was independently associated with the following biochemical variations: phosphorus >40 mg/L (odds ratio [OR], 3.35, 95% confidence interval [CI], 1.83–6.14), creatinine >10.1 mg/L (OR, 3.22, 2.28–4.54), and urea nitrogen (UN) >0.52 g/L (OR, 2.65, 95% CI, 1.89–3.73). ACEI/ARB use was independently associated with acute kidney injury stage ≥1 (OR, 3.28, 95% CI, 2.17–4.94). The daily dose of ACEI/ARB was independently associated with altered kidney markers with an increased risk of +25 to +31% per each 10 mg increment of lisinopril-dose equivalent. In multivariable multilevel modeling, UN >0.52 g/L was independently associated with the risk of acute respiratory failure (OR, 3.54, 95% CI, 1.05–11.96).

Conclusions

Patients chronically treated with ACEI/ARB who have severe COVID-19 are at increased risk of acute kidney injury. In these patients, the increase in UN associated with ACEI/ARB use could predict the development of acute respiratory failure.

Traditional Usage of Wild Fauna among the Local Inhabitants of Ladakh, Trans-Himalayan Region

Zootherapy is accepted all around the globe not only in ancient cultures but different animal derived medicines are also part of the practice in the modern health care systems. The present study assessed the traditional ethnozoological usage of wild animals by local inhabitants in Ladakh region, India, and the reference data for scientific approaches for protection of faunal diversity in trans-Himalayas. The ethnozoological documentation of the animals in Ladakh was carried out through semistructured and close-ended questionnaire surveys and interviews. Multivariate ecological community analysis was used to elucidate the relationship between ethnozoological usage and animal species. Our results showed three animal usage clusters with 32% similarity. Moreover, the similarity in animal usage between digging tools, trophy, handle of tools, decoration, and matting, showed less than 32% of similarity. The highest priority of local people was for food followed by decoration and medicinal usage. The most frequently used animal parts were meat followed by fur and horn. Medicinal uses of 48% of the reported species, i.e., Alectoris chukar (chukar), Cuon alpinus (Asiatic wild dog), Lepus oiostolus (hares), Marmota himalayana (marmots), Ovis aries vignei (Ladakh urial), Pantholops hodgsonii (Tibetan antelope), Procapra picticaudata (Tibetan gazelle), Pseudois nayaur (blue sheep), Tetraogallus himalayensis (Himalayan snow), Tetraogallus tibetanus (Tibetan snow cock), and Lutra lutra (common otter) were reported for the first time from this region. Our study provides innovative information regarding the ethnozoological knowledge in the Ladakh region and reference data for policymakers, researchers, land managers, common public, and the other stakeholders to develop logical and scientific approaches for sustainable use of faunal diversity in hotspot regions like trans-Himalayas and other similar biodiversity-rich sites.

Comparison of the clinical manifestations between different age groups of patients with overseas imported COVID-19

The current study investigated the clinical manifestations and outcomes of different age groups of patients with overseas imported COVID-19. In total, 53 COVID-19 patients admitted to the designated Beijing Xiaotangshan Hospital between March 16 and April 15 of 2020 were included. Based on the percentage of disease aggravation during hospital stay according to CT, the patients were divided into two groups: ≤40 years (group A; n = 41) and >40 years (group B; n = 12). The demographic data, epidemiological history, disease courses, potential complications, clinical symptoms, lab indices, chest CT outcomes, treatment protocols and turnovers of the two groups were compared. According to clinical typing, compared with group A, group B had a significantly greater proportion of the common type of COVID-19 (P<0.05) and greater comorbidity of type 2 diabetes (P<0.001). The two groups presented significantly different lab indices. Group B showed significantly more frequent CT abnormalities, with greater proportions of multiple lesions and bilateral lung involvement (P<0.05). During hospitalization, group B had a greater proportion of disease aggravation according to CT (P<0.01). Compared with group A, group B received a significantly greater proportion of antiviral therapy and presented a significantly greater occurrence of adverse drug reactions (P<0.05). The two groups did not significantly differ in time from admission to clinical symptom improvement or from disease onset to negative outcomes according to nucleic acid testing, the appearance of IgG or the appearance of IgM. They also did not significantly differ in length of stay. Older imported COVID-19 patients, particularly those with type 2 diabetes, showed a broader pulmonary extent and faster development of the disease, more severe pathogenetic conditions and a greater risk of developing a critically severe type. Increased attention should be given to this population in clinical practice.

Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for rapid and accurate nucleic acid detection at the point of care. Here, we report an amplification-free nucleic acid immunoassay, implemented on a lateral flow strip, for the fluorescence detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in less than one hour. The assay uses DNA probes that are designed to bind to the conserved open reading frame 1ab (ORF1ab), envelope protein (E) and the nucleocapsid (N) regions of the SARS-CoV-2 genome, and a fluorescent-nanoparticle-labelled monoclonal antibody that binds to double-stranded DNA-RNA hybrids. In a multi-hospital randomized double-blind trial involving 734 samples (593 throat swabs and 141 sputum) provided by 670 individuals, the assay achieved sensitivities of 100% and specificities of 99% for both types of sample (ground truth was determined using quantitative PCR with reverse transcription). The inexpensive amplification-free detection of SARS-CoV-2 RNA should facilitate the rapid diagnosis of COVID-19 at the point of care.