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1.
Transfusion ; 60(10): 2441-2447, 2020 10.
Article in English | MEDLINE | ID: covidwho-1388415

ABSTRACT

BACKGROUND: In the pandemic, testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time polymerase chain reaction is one of the pillars on which countermeasures are based. Factors limiting the output of laboratories interfere with the effectiveness of public health measures. Conserving reagents by pooling samples in low-probability settings is proposed but may cause dilution and loss of sensitivity. Blood transfusion services had experience in performance of high throughput nucleic acid testing (NAT) analysis and can support the national health system by screening of the inhabitants for SARS-COV-2. METHODS: We evaluated a new approach of a multiple-swab method by simultaneously incubating multiple respiratory swabs in a single tube. Analytical sensitivity was constant up to a total number of 50 swabs. It was consequently applied in the testing of 50 symptomatic patients (5-sample pools) as well as 100 asymptomatic residents of a nursing home (10-sample pools). RESULTS: The novel method did not cause false-negative results with nonsignificantly differing cycle threshold values between single-swab and multiple-swab NAT. In two routine applications, all minipools containing positive patient samples were correctly identified. CONCLUSIONS: The new method enables countries to increase the total number of testing significantly. The multiple-swab method is able to screen system relevant groups of employees frequently. The example in Germany shows that blood transfusion services can support general health systems with their experience in NAT and their high-throughput instruments. Screening of a huge number of inhabitants is currently the only option to prevent a second infection wave and enable exit strategies in many countries.


Subject(s)
SARS-CoV-2/pathogenicity , COVID-19/virology , Germany , Humans , Nucleic Acid Amplification Techniques/methods , Specimen Handling/methods
2.
Front Pharmacol ; 11: 579330, 2020.
Article in English | MEDLINE | ID: covidwho-1389228

ABSTRACT

The Syrian golden hamster (Mesocricetus auratus) has recently been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. However, lack of knowledge about the tissue-specific expression pattern of various proteins in these animals and the unavailability of reagents like antibodies against this species hampers these models' optimal use. The major objective of our current study was to analyze the tissue-specific expression pattern of angiotensin-converting enzyme 2, a proven functional receptor for SARS-CoV-2 in different organs of the hamster. Using two different antibodies (MA5-32307 and AF933), we have conducted immunoblotting, immunohistochemistry, and immunofluorescence analysis to evaluate the ACE2 expression in different tissues of the hamster. Further, at the mRNA level, the expression of Ace2 in tissues was evaluated through RT-qPCR analysis. Both the antibodies detected expression of ACE2 in kidney, small intestine, tongue, and liver. Epithelium of proximal tubules of kidney and surface epithelium of ileum expresses a very high amount of this protein. Surprisingly, analysis of stained tissue sections showed no detectable expression of ACE2 in the lung or tracheal epithelial cells. Similarly, all parts of the large intestine were negative for ACE2 expression. Analysis of tissues from different age groups and sex didn't show any obvious difference in ACE2 expression pattern or level. Together, our findings corroborate some of the earlier reports related to ACE2 expression patterns in human tissues and contradict others. We believe that this study's findings have provided evidence that demands further investigation to understand the predominant respiratory pathology of SARS-CoV-2 infection and disease.

3.
Materials (Basel) ; 13(13)2020 Jun 27.
Article in English | MEDLINE | ID: covidwho-1332160

ABSTRACT

The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young's moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

4.
J Family Med Prim Care ; 9(12): 6061-6067, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1244952

ABSTRACT

Background: Visceral leishmaniasis in human (VLH) also known as kala-azar is a neglected disease of humans that mainly occurs in more than 50 countries mostly located in the Eastern Mediterranean and the Northern America. Objective: The purpose of this study was to determine the temporal patterns and predict of occurrence of VL in Ardabil Province, in northwestern Iran using autoregressive integrated moving average (ARIMA) models. Methods: This descriptive study employed yearly and monthly data of 602 cases of VLH in the province between January 2000 to December 2019, which was provided by the leishmaniasis national surveillance system. The monthly occurrences case constructed the ARIMA model of time-series model. The insignificance of the correlation in the lags of 12, 24 and 36 months, and Chi-square test showed the occurrence of VLH does not have a seasonal pattern. Eleven potential ARIMA models were examined for VLH cases. Finally, the best model was selected with the lower Akaike Information Criteria (AIC) and Bayesian information criterion (BIC) value. Then, the selected model was used to forecast frequency of monthly occurrences case. The forecasting precision was estimated by mean absolute percentage error (MAPE). Data analysis was performed using Stata14 and its package time series analysis. Results: ARIMA (5, 0, 1) model with AIC (25.7) and BIC (43.35) was selected. The MAPE value was 26.89% and the portmanteau test for white noise was (Q = 23.02, P = 0.98) for the residuals of the selected model showed that the data were fully modelled. The total cumulative VLH cases in the next 24 months' in Ardabil province predicted 14 cases (95% CI: 4-54 case). Conclusion: The ARIMA (5, 0, 1) model can be a useful tool to predict VLH cases as early warning system and the results are helpful for policy makers and primary care physicians in the readiness of public health problems before the outbreak of the disease.

5.
Front Microbiol ; 11: 1552, 2020.
Article in English | MEDLINE | ID: covidwho-686841

ABSTRACT

Respiratory virus infections are one of the major causes of acute respiratory disease or exacerbation of chronic obstructive pulmonary disease (COPD). However, next-generation sequencing has not been used for routine viral detection in clinical respiratory samples owing to its sophisticated technology. Here, several pharyngeal samples with COPD were collected to enrich viral particles using an optimized method (M3), which involved M1 with centrifugation, filtration, and concentration, M2 (magnetic beads) combined with mixed nuclease digestion, and M4 with no pretreatment as a control. Metagenomic sequencing and bioinformatics analyses showed that the M3 method for viral enrichment was superior in both viral sequencing composition and viral taxa when compared to M1, M2, and M4. M3 acquired the most viral reads and more complete sequences within 15-h performance, indicating that it might be feasible for viral detection in multiple respiratory samples in clinical practice. Based on sequence similarity analysis, 12 human viruses, including nine Anelloviruses and three coronaviruses, were characterized. Coronavirus OC43 with the largest number of viral reads accounted for nearly complete (99.8%) genome sequences, indicating that it may be a major viral pathogen involved in exacerbation of COPD.

6.
BMJ Open ; 10(12): e039560, 2020 12 17.
Article in English | MEDLINE | ID: covidwho-1102180

ABSTRACT

INTRODUCTION: Ageing-related processes such as cellular senescence are believed to underlie the accumulation of diseases in time, causing (co)morbidity, including cancer, thromboembolism and stroke. Interfering with these processes may delay, stop or reverse morbidity. The aim of this study is to investigate the link between (co)morbidity and ageing by exploring biomarkers and molecular mechanisms of disease-triggered deterioration in patients with pancreatic ductal adenocarcinoma (PDAC) and (thromboembolic) ischaemic stroke (IS). METHODS AND ANALYSIS: We will recruit 50 patients with PDAC, 50 patients with (thromboembolic) IS and 50 controls at Rostock University Medical Center, Germany. We will gather routine blood data, clinical performance measurements and patient-reported outcomes at up to seven points in time, alongside in-depth transcriptomics and proteomics at two of the early time points. Aiming for clinically relevant biomarkers, the primary outcome is a composite of probable sarcopenia, clinical performance (described by ECOG Performance Status for patients with PDAC and the Modified Rankin Scale for patients with stroke) and quality of life. Further outcomes cover other aspects of morbidity such as cognitive decline and of comorbidity such as vascular or cancerous events. The data analysis is comprehensive in that it includes biostatistics and machine learning, both following standard role models and additional explorative approaches. Prognostic and predictive biomarkers for interventions addressing senescence may become available if the biomarkers that we find are specifically related to ageing/cellular senescence. Similarly, diagnostic biomarkers will be explored. Our findings will require validation in independent studies, and our dataset shall be useful to validate the findings of other studies. In some of the explorative analyses, we shall include insights from systems biology modelling as well as insights from preclinical animal models. We anticipate that our detailed study protocol and data analysis plan may also guide other biomarker exploration trials. ETHICS AND DISSEMINATION: The study was approved by the local ethics committee (Ethikkommission an der Medizinischen Fakultät der Universität Rostock, A2019-0174), registered at the German Clinical Trials Register (DRKS00021184), and results will be published following standard guidelines.


Subject(s)
Adenocarcinoma , Brain Ischemia , Ischemic Stroke , Pancreatic Neoplasms , Stroke , Adenocarcinoma/epidemiology , Aging , COVID-19 , Cellular Senescence , Cohort Studies , Comorbidity , Female , Germany/epidemiology , Humans , Male , Pancreatic Neoplasms/epidemiology , Prospective Studies , Quality of Life , SARS-CoV-2 , Stroke/epidemiology
7.
iScience ; 23(10): 101611, 2020 Oct 23.
Article in English | MEDLINE | ID: covidwho-1065230

ABSTRACT

The molecular mechanisms of cytokine storm in patients with severe COVID-19 infections are poorly understood. To uncover these events, we performed transcriptome analyses of lung biopsies from patients with COVID-19, revealing a gene enrichment pattern similar to that of PPARγ-knockout macrophages. Single-cell gene expression analysis of bronchoalveolar lavage fluids revealed a characteristic trajectory of PPARγ-related disturbance in the CD14+/CD16+ cells. We identified a correlation with the disease severity and the reduced expression of several members of the PPARγ complex such as EP300, RXRA, RARA, SUMO1, NR3C1, and CCDC88A. ChIP-seq analyses confirmed repression of the PPARγ-RXRA-NR3C1 cistrome in COVID-19 lung samples. Further analysis of protein-protein networks highlighted an interaction between the PPARγ-associated protein SUMO1 and a nucleoprotein of the SARS virus. Overall, these results demonstrate for the first time the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte/macrophage-mediated inflammatory storm.

8.
Front Neurol ; 11: 615172, 2020.
Article in English | MEDLINE | ID: covidwho-1063344

ABSTRACT

Self-perceived unmet needs in people with typical and atypical parkinsonism (PwP) and their caregivers, support network, personalized ways to address self-perceived unmet needs during confinement, as well as the prevalence of self-reported COVID-19 related symptoms, confirmed SARS-CoV-2 infection, and self-reported COVID-19 related hospitalization in Luxembourg and the Greater Region were assessed. From 18th March to 10th April 2020, 679 PwP were contacted by phone. Data was collected in the form of a semi-structured interview. The thematic synthesis identified 25 themes where PwP need to be supported in order to cope with consequences of the pandemic, and to adapt their daily and health-related activities. The present work highlights that in the context of personalized medicine, depending on the individual needs of support of the patient the identified self-perceived unmet needs were addressed in various ways ranging from one-directed information over interaction up to proactive counseling and monitoring. Family and health professionals, but also other support systems were taking care of the unmet needs of PwP (e.g., shopping, picking-up medication, etc.) during the pandemic. 7/606 PwP (1.15%) reported COVID-19 related symptoms, 4/606 (0.66%) underwent a rRT-PCR-based diagnostic test and 2/606 (0.33%) were confirmed as SARS-CoV-2 positive. None of these PwP reported being hospitalized due to COVID-19. Our results will allow health professionals to expand their services in a meaningful way i.e., personalize their support in the identified themes and thus improve the healthcare of PwP in times of crisis.

10.
Am J Transl Res ; 12(4): 1348-1354, 2020.
Article in English | MEDLINE | ID: covidwho-1024940

ABSTRACT

BACKGROUND: Since December 2019, there had been an outbreak of COVID-19 in Wuhan, China. At present, diagnosis COVID-19 were based on real-time RT-PCR, which have to be performed in biosafe laboratory and is unsatisfactory for suspect case screening. Therefore, there is an urgent need for rapid diagnostic test for COVID-19. OBJECTIVE: To evaluate the diagnostic performance and clinical utility of the colloidal gold immunochromatography assay for SARS-Cov-2 specific IgM/IgG anti-body detection in suspected COVID-19 cases. METHODS: In the prospective cohort, 150 patients with fever or respiratory symptoms were enrolled in Taizhou Public Health Medical Center, Taizhou Hospital, Zhejiang province, China, between January 20 to February 2, 2020. All patients were tested by the colloidal gold immunochromatography assay for COVID-19. At least two samples of each patient were collected for RT-PCR assay analysis, and the PCR results were performed as the reference standard of diagnosis. Meanwhile 26 heathy blood donor were recruited. The sensitivity and specificity of the immunochromatography assay test were evaluated. Subgroup analysis were performed with respect to age, sex, period from symptom onset and clinical severity. RESULTS: The immunochromatography assay test had 69 positive result in the 97 PCR-positive cases, achieving sensitivity 71.1% [95% CI 0.609-0.797], and had 2 positive result in the 53 PCR-negative cases, achieving specificity 96.2% [95% CI 0.859-0.993]. In 26 healthy donor blood samples, the immunochromatography assay had 0 positive result. In subgroup analysis, the sensitivity was significantly higher in patients with symptoms more than 14 days 95.2% [95% CI 0.741-0.998] and patients with severe clinical condition 86.0% [95% CI 0.640-0.970]. CONCLUSIONS: The colloidal gold immunochromatography assay for SARS-Cov-2 specific IgM/IgG anti-body had 71.1% sensitivity and 96.2% specificity in this population, showing the potential for a useful rapid diagnosis test for COVID-19. Further investigations should be done to evaluate this assay in variety of clinical settings and populations.

11.
Dis Markers ; 2020: 8869424, 2020.
Article in English | MEDLINE | ID: covidwho-1024275

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. The presence of viral RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients' viral load. Since the demand for laboratory reagents has increased, there has been a worldwide shortage of RNA extraction kits. We, therefore, developed a fast and cost-effective viral genome isolation method that, combined with quantitative RT-PCR assay, detects SARS-CoV-2 RNA in patient samples. The method relies on the addition of Proteinase K followed by a controlled heat-shock incubation and, then, E gene evaluation by RT-qPCR. It was validated for sensitivity, specificity, linearity, reproducibility, and precision. It detects as low as 10 viral copies/sample, is rapid, and has been characterized in 60 COVID-19-infected patients. Compared to automated extraction methods, our pretreatment guarantees the same positivity rate with the advantage of shortening the time of the analysis and reducing its cost. This is a rapid workflow meant to aid the healthcare system in the rapid identification of infected patients, such as during a pathogen-related outbreak. For its intrinsic characteristics, this workflow is suitable for large-scale screenings.


Subject(s)
COVID-19 Testing/methods , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Coronavirus Envelope Proteins/genetics , Humans , Limit of Detection , Nasopharynx/virology , Sensitivity and Specificity , Workflow
12.
Int J Nanomedicine ; 15: 10425-10434, 2020.
Article in English | MEDLINE | ID: covidwho-999917

ABSTRACT

Purpose: The public fear associated with the novel coronavirus (SARS-CoV-2) pandemic has triggered recently a significant proliferation of supplements touted as potential cures against bacteria and viruses. Colloidal silver has particularly benefited from this rush given its empirically and scientifically documented anti-bacterial and anti-viral actions. The lack of standards in the unregulated supplements industry remains a major roadblock in evaluating the quality and consistency of marketed products or assessing the accuracy of the information provided by manufacturers. This study is the first scientifically rigorous attempt to evaluate commercial silver colloidal products offered for sale on the internet. Methods: Fourteen of the most popular colloidal silver products purchased from Amazon (www.amazon.com) were evaluated using state-of-the-art analytical techniques widely accepted as gold standards for investigating the properties (size, shape) and the dispersion of silver nanoparticles. Results: Commercial samples were analysed using UV-Vis, FE-SEM and AAS techniques. In general, the Ag concentration was very close to those claimed by the manufacturer. The colorless product shows no absorbance in the UV-Vis analysis. The FESEM and STEM images confirmed the conclusions of the UV-Vis analysis. Conclusion: The results of this evaluation show clearly that 70% of the commercial products evaluated contain only ionic silver. Despite the evidence showing that silver nanoparticles are not present, eight of these products are promoted by the manufacturers as 'colloidal silver'. Considering the extensive scientific research showing major differences between silver ionic and silver nanoparticles in terms of mechanisms of action, efficacy and safety, it is clear that this misrepresentation impacts the consumers and must be addressed. This study serves as blueprint for a scientific protocol to be followed by manufacturers for characterizing their silver supplements.


Subject(s)
Anti-Bacterial Agents/chemistry , Silver/chemistry , Anti-Bacterial Agents/adverse effects , Anti-Bacterial Agents/pharmacology , Humans , Metal Nanoparticles/chemistry , Safety , Silver/adverse effects , Silver/pharmacology
13.
Eur J Pharmacol ; 887: 173594, 2020 Nov 15.
Article in English | MEDLINE | ID: covidwho-996862

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, more commonly COVID-19 has emerged as a world health pandemic. There are couples of treatment methods for COVID-19, however, well-established drugs and vaccines are urgently needed to treat the COVID-19. The new drug discovery is a tremendous challenge; repurposing of existing drugs could shorten the time and expense compared with de novo drug development. In this study, we aimed to decode molecular signatures and pathways of the host cells in response to SARS-CoV-2 and the rapid identification of repurposable drugs using bioinformatics and network biology strategies. We have analyzed available transcriptomic RNA-seq COVID-19 data to identify differentially expressed genes (DEGs). We detected 177 DEGs specific for COVID-19 where 122 were upregulated and 55 were downregulated compared to control (FDR<0.05 and logFC ≥ 1). The DEGs were significantly involved in the immune and inflammatory response. The pathway analysis revealed the DEGs were found in influenza A, measles, cytokine signaling in the immune system, interleukin-4, interleukin -13, interleukin -17 signaling, and TNF signaling pathways. Protein-protein interaction analysis showed 10 hub genes (BIRC3, ICAM1, IRAK2, MAP3K8, S100A8, SOCS3, STAT5A, TNF, TNFAIP3, TNIP1). The regulatory network analysis showed significant transcription factors (TFs) that target DEGs, namely FOXC1, GATA2, YY1, FOXL1, NFKB1. Finally, drug repositioning analysis was performed with these 10 hub genes and showed that in silico validated three drugs with molecular docking. The transcriptomics signatures, molecular pathways, and regulatory biomolecules shed light on candidate biomarkers and drug targets which have potential roles to manage COVID-19. ICAM1 and TNFAIP3 were the key hubs that have demonstrated good binding affinities with repurposed drug candidates. Dabrafenib, radicicol, and AT-7519 were the top-scored repurposed drugs that showed efficient docking results when they tested with hub genes. The identified drugs should be further evaluated in molecular level wet-lab experiments in prior to clinical studies in the treatment of COVID-19.


Subject(s)
Coronavirus Infections/drug therapy , Coronavirus Infections/genetics , Drug Repositioning , Epithelial Cells/drug effects , Lung/cytology , Pneumonia, Viral/drug therapy , Pneumonia, Viral/genetics , Transcriptome , Antiviral Agents/therapeutic use , COVID-19 , Cells, Cultured , Computational Biology , Computer Simulation , Gene Expression Regulation/genetics , Humans , Pandemics , Signal Transduction/drug effects , Signal Transduction/genetics , Transcription Factors/genetics
14.
Virol J ; 17(1): 197, 2020 12 28.
Article in English | MEDLINE | ID: covidwho-992505

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30 to 60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. METHOD: In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. RESULT: The limit of detection (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI: 363.23-1145.69) for ORF1ab and 528.1 (95% CI: 347.7-1248.7) for N, 401.8 (95% CI: 284.8-938.3) for ORF1ab and 336.8 (95% CI: 244.6-792.5) for N, and 194.74 (95% CI: 139.7-430.9) for ORF1ab and 189.1 (95% CI: 130.9-433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. CONCLUSION: In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.


Subject(s)
COVID-19/diagnosis , SARS-CoV-2/isolation & purification , COVID-19/virology , Humans , Limit of Detection , Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity
15.
J Clin Microbiol ; 59(1)2020 12 17.
Article in English | MEDLINE | ID: covidwho-991749

ABSTRACT

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT ) values correlated with greater SARS-CoV-2 read recovery by mNGS (R 2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.


Subject(s)
Betacoronavirus/isolation & purification , COVID-19/diagnosis , Coronavirus OC43, Human/isolation & purification , Influenza A virus/isolation & purification , Metapneumovirus/isolation & purification , SARS-CoV-2/isolation & purification , Betacoronavirus/genetics , COVID-19 Nucleic Acid Testing/methods , Coinfection/virology , Coronavirus OC43, Human/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Humans , Influenza A virus/genetics , Metagenome , Metagenomics , Metapneumovirus/genetics , SARS-CoV-2/genetics
16.
Int J Neurosci ; : 1-6, 2020 Dec 30.
Article in English | MEDLINE | ID: covidwho-983893

ABSTRACT

BACKGROUND: The complications of coronavirus disease 2019 (COVID-19), the clinical entity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are not limited to the respiratory system. Leukoencephalopathy with microbleeds is increasingly seen in patients with COVID-19. New information is needed to delineate better the clinical implications of this infectious disease. CASE REPORT: A 46-year-old man with confirmed SARS-CoV-2 infection was admitted to the intensive care unit (ICU) with severe COVID-19. After transfer to the general wards, the patient was noted drowsy, disorientated, with slow thinking and speech. A brain MRI showed bilateral symmetrical hyperintense lesions in the deep and subcortical whiter matter, involving the splenium of the corpus callosum, as well as multiple microhemorrhages implicating the splenium and subcortical white matter. No contrast-enhanced lesions were observed in brain CT or MRI. CSF analysis showed no abnormalities, including a negative rtRT-PCR for SARS-CoV-2. An outpatient follow-up visit showed near-complete clinical recovery and resolution of the hyperintense lesions on MRI, without microbleeds change. CONCLUSION: We present the case of a survivor of severe COVID-19 who presented diffuse posthypoxic leukoencephalopathy, and microbleeds masquerading as acute necrotizing encephalopathy. We postulate that this kind of cerebral vasogenic edema with microbleeds could be the consequence of hypoxia, inflammation, the prothrombotic state and medical interventions such as mechanical ventilation and anticoagulation.

17.
Sci Rep ; 10(1): 21617, 2020 12 10.
Article in English | MEDLINE | ID: covidwho-971935

ABSTRACT

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.


Subject(s)
COVID-19/genetics , Evolution, Molecular , Host Specificity , Recombination, Genetic , SARS-CoV-2/genetics , Animals , COVID-19/epidemiology , Chiroptera , Humans , Pangolins
19.
Nat Commun ; 11(1): 6272, 2020 12 09.
Article in English | MEDLINE | ID: covidwho-965783

ABSTRACT

Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. We report that, despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.


Subject(s)
Nanopore Sequencing/methods , SARS-CoV-2 , Whole Genome Sequencing/methods , COVID-19/diagnosis , COVID-19/virology , Genome, Viral , Humans , RNA, Viral , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
20.
Medicine (Baltimore) ; 99(49): e23401, 2020 Dec 04.
Article in English | MEDLINE | ID: covidwho-963622

ABSTRACT

BACKGROUND: Corona virus disease 2019 (COVID-19) is an epidemic respiratory infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 infection. Now it is popular all over the world on a large scale. COVID-19 has the characteristics of rapid transmission, atypical clinical symptoms, easy missed diagnosis and misdiagnosis, and so on. which has seriously affected social and economic development and people's health. Severe acute respiratory syndrome corona virus type 2 infection may lead to systemic cytokine storm, which leads to a sharp deterioration of the condition of ordinary patients. At present, no specific drug has been found in the clinical treatment of covid-19, while Xuebijing injection has been widely used in severe patients in China as a traditional Chinese medicine. The aim of this study is to assess the effificacy and safety of Xuebijing injection for COVID-19. METHODS: Before the research, we conducted a comprehensive search on relevant websites. Two professional researchers will gradually screen, read the title, abstract and full text if necessary, and independently select qualified documents according to the inclusion and exclusion criteria. We will conduct a meta-analysis of the results related to COVID-19 to assess the risks of bias and data extraction. The heterogeneity of data will be studied by Cochrane X and I tests. The evaluation of publication bias will be carried out by funnel chart analysis and Eger test. RESULTS: This review will be disseminated in print by peer-review. CONCLUSION: Our research is to scientifically analyze the clinical evidence of Xuebijing injection in treating severe COVID-19 patients.


Subject(s)
COVID-19/drug therapy , Drugs, Chinese Herbal/therapeutic use , COVID-19/physiopathology , Clinical Trials as Topic , Drugs, Chinese Herbal/administration & dosage , Drugs, Chinese Herbal/adverse effects , Humans , Infusions, Intravenous , Medicine, Chinese Traditional , Pandemics , Research Design , SARS-CoV-2 , Severity of Illness Index
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