### Overview

MeSH Disease

Infections (331)

Pneumonia (180)

Death (114)

Human Phenotype

Pneumonia (231)

Fever (70)

Cough (38)

Hypertension (27)

Falls (24)

Transmission

Seroprevalence
displaying 1381 - 1390 records in total 1730
records per page

### A Smartphone enabled Approach to Manage COVID-19 Lockdown and Economic Crisis

Authors: Halgurd S. Maghdid; Kayhan Zrar Ghafoor

id:2004.12240v2 Date: 2020-04-25 Source: arXiv

The emergence of novel COVID-19 causing an overload in health system and high mortality rate. The key priority is to contain the epidemic and prevent the infection rate. In this context, many countries are now in some degree of lockdown to ensure extreme social distancing of entire population and hence slowing down the epidemic spread. Further, authorities use case quarantine strategy and manual second/third contact-tracing TRANS to contain the COVID-19 disease. However, manual contact tracing TRANS is time consuming and labor-intensive task which tremendously overload public health systems. In this paper, we developed a smartphone-based approach to automatically and widely trace the contacts TRANS for confirmed COVID-19 cases. Particularly, contact-tracing TRANS approach creates a list of individuals in the vicinity and notifying contacts or officials of confirmed COVID-19 cases. This approach is not only providing awareness to individuals they are in the proximity to the infected area, but also tracks the incidental contacts that the COVID-19 carrier TRANS might not recall SERO. Thereafter, we developed a dashboard to provide a plan for government officials on how lockdown/mass quarantine can be safely lifted, and hence tackling the economic crisis. The dashboard used to predict the level of lockdown area based on collected positions and distance measurements of the registered users in the vicinity. The prediction model uses K-means algorithm as an unsupervised machine learning technique for lockdown management.

### Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2

Authors: Marie C Smithgall; Ioana Scherberkova; Susan Whittier; Daniel Green

doi:10.1101/2020.04.22.055327 Date: 2020-04-25 Source: bioRxiv

The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. This study compared two recently-authorized rapid tests SERO, Cepheid Xpert Xpress SARS-CoV-2 MESHD and Abbott ID Now SARS-CoV-2 to the Roche cobas SARS-CoV-2 assay. A total of 113 nasopharyngeal swabs were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance SERO of ID Now for direct swabs.

### Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR

Authors: Ignacio Torres; Eliseo Albert; David Navarro

doi:10.1101/2020.04.22.20075598 Date: 2020-04-25 Source: medRxiv

Systematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing TRANS in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission TRANS of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity SERO of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.

### Modelling the transmission TRANS dynamics of COVID-19 in six high burden countries

Authors: Azizur Rahman; Md Abdul Kuddus

doi:10.1101/2020.04.22.20075192 Date: 2020-04-25 Source: medRxiv

The new coronavirus disease MESHD, officially known as COVID-19, originated in China in 2019 and has since spread around the globe. We presented a modified Susceptible-Latent-Infected-Removed (SLIR) compartmental model of COVID-19 disease transmission TRANS with nonlinear incidence during the epidemic period. We provided the model calibration to estimate parameters with day wise corona virus (COVID-19) data i.e. reported cases by worldometer from the period of 15th February to 30th March, 2020 in six high burden countries including Australia, Italy, Spain, USA, UK and Canada. We estimate transmission TRANS rates for each countries and found that the highest transmission TRANS rate country in Spain, which may be increase the new cases and deaths MESHD in Spain than the other countries. Sensitivity SERO analysis was used to identify the most important parameters through the partial rank correlation coefficient method. We found that the transmission TRANS rate of COVID-19 had the largest influence on the prevalence SERO. We also provides the prediction of new cases in COVID-19 until May 18, 2020 using the developed model and recommends, control strategies of COVID-19. The information that we generated from this study would be useful to the decision makers of various organizations across the world including the Ministry of Health in Australia, Italy, Spain, USA, UK and Canada to control COVID-19.

### Model the transmission TRANS dynamics of COVID-19 propagation with public health intervention

Authors: Dejen Ketema Mamo

doi:10.1101/2020.04.22.20075184 Date: 2020-04-25 Source: medRxiv

In this work, a researcher develop $SHEIQRD$ (Susceptible-Stay at home-Exposed-Infected-Quarantine-Recovery-Death) coronavirus pandemic spread model. The disease-free and endemic equilibrium points are calculated and analyzed. The basic reproductive number TRANS $R_0 TRANS$ is derived and its sensitivity SERO analysis is done. COVID-19 pandemic spread is die out when $R_0 TRANS\leq 1$ and its persist in the community whenever $R_0 TRANS>1$. Efficient stay at home rate, high coverage of precise identification and isolation of expose and infected individuals, and redaction of transmission TRANS and stay at home return rate can be mitigate the pandemics. Finally, theoretical analysis and numerical results are consistent.

### Optimized qRT-PCR approach for the detection of intra- and extracellular SARS-CoV-2 RNAs

Authors: Tuna Toptan; Sebastian Hoehl; Sandra Westhaus; Denisa Bojkova; Annemarie Berger; Bjoern Rotter; Klaus Hoffmeier; Sandra Ciesek; Marek Widera

doi:10.1101/2020.04.20.052258 Date: 2020-04-25 Source: bioRxiv

The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease MESHD COVID-19 which has become a global concern due to its rapid spread. Meanwhile, increased demand in testing has led to shortage of reagents, supplies, and compromised the performance SERO of diagnostic laboratories in many countries. Both the world health organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate interpretation of the test results especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in the diagnostics as well as in research labs using a low cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infection MESHD and performed RT-PCR assays along with successive dilutions of RNA standards to determine the limit of detection. We identified an M-gene binding primer and probe pair highly suitable for quantitative detection of SARS-CoV-2 RNA for diagnostic and research purposes.

### Detection of COVID-19 Infection from Routine Blood SERO Exams with Machine Learning: a Feasibility Study

Authors: Davide Brinati; Andrea Campagner; Davide Ferrari; Massimo Locatelli; Giuseppe Banfi; Federico Cabitza

doi:10.1101/2020.04.22.20075143 Date: 2020-04-25 Source: medRxiv

Background - The COVID-19 pandemia due to the SARS-CoV-2 coronavirus MESHD, in its first 4 months since its outbreak, has to date reached more than 200 countries worldwide with more than 2 million confirmed cases TRANS (probably a much higher number of infected), and almost 200,000 deaths. Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection MESHD, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Thus there is a need for alternative, faster, less expensive and more accessible tests. Material and methods - We developed two machine learning classification models using hematochemical values from routine blood SERO exams (namely: white blood SERO cells counts, and the platelets, CRP, AST, ALT, GGT, ALP MESHD, LDH plasma SERO levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. Of these patients, 177 resulted positive, whereas 102 received a negative response. Results - We have developed two machine learning models, to discriminate between patients who are either positive or negative to the SARS-CoV-2: their accuracy ranges between 82% and 86%, and sensitivity SERO between 92% e 95%, so comparably well with respect to the gold standard. We also developed an interpretable Decision Tree model as a simple decision aid for clinician interpreting blood SERO tests (even off-line) for COVID-19 suspect cases. Discussion - This study demonstrated the feasibility and clinical soundness of using blood SERO tests analysis and machine learning as an alternative to rRT-PCR for identifying COVID-19 positive patients. This is especially useful in those countries, like developing ones, suffering from shortages of rRT-PCR reagents and specialized laboratories. We made available a Web-based tool for clinical reference and evaluation. This tool is available at https://covid19- blood SERO-ml.herokuapp.com.

### A Light CNN for detecting COVID-19 from CT scans of the chest

Authors: Matteo Polsinelli; Luigi Cinque; Giuseppe Placidi

id:2004.12837v1 Date: 2020-04-24 Source: arXiv

OVID-19 is a world-wide disease that has been declared as a pandemic by the World Health Organization. Computer Tomography (CT) imaging of the chest seems to be a valid diagnosis tool to detect COVID-19 promptly and to control the spread of the disease TRANS. Deep Learning has been extensively used in medical imaging and convolutional neural networks (CNNs) have been also used for classification of CT images. We propose a light CNN design based on the model of the SqueezeNet, for the efficient discrimination of COVID-19 CT images with other CT images (community-acquired pneumonia HP and/or healthy images). On the tested datasets, the proposed modified SqueezeNet CNN achieved 83.00\% of accuracy, 85.00\% of sensitivity SERO, 81.00\% of specificity, 81.73\% of precision and 0.8333 of F1Score in a very efficient way (7.81 seconds medium-end laptot without GPU acceleration). Besides performance SERO, the average classification time is very competitive with respect to more complex CNN designs, thus allowing its usability also on medium power computers. In the next future we aim at improving the performances SERO of the method along two directions: 1) by increasing the training dataset (as soon as other CT images will be available); 2) by introducing an efficient pre-processing strategy.

### Comparison of commercial RT-PCR diagnostic kits for COVID-19

Authors: Puck B van Kasteren; Bas van der Veer; Sharon van den Brink; Lisa Wijsman; Jorgen de Jonge; Anne-Marie van den Brandt; Richard Molenkamp; Chantal B.E.M. Reusken; Adam Meijer

doi:10.1101/2020.04.22.056747 Date: 2020-04-24 Source: bioRxiv

The final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected MESHD individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance SERO has not yet been independently assessed. The aim of this study was to compare basic analytical and clinical performance SERO of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene). We used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95% limit of detection (LOD95%). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n=16) for a preliminary evaluation of clinical sensitivity SERO. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n=6) and a panel of RNA from related human coronaviruses to evaluate assay specificity. PCR efficiency was [≥]96% for all assays and the estimated LOD95% varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene. We conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories.

### Performance SERO of fabrics for home-made masks against spread of respiratory infection MESHD through droplets: a quantitative mechanistic study

Authors: Onur Aydin; Md Abul Bashar Emon; Shyuan Cheng; Liu Hong; Leonardo P. Chamorro; M Taher A Saif

doi:10.1101/2020.04.19.20071779 Date: 2020-04-24 Source: medRxiv

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

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 All None MeSH Disease Human Phenotype Transmission Seroprevalence

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