scholarly journals A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

2020 ◽  
Author(s):  
Brian Glenn St Hilaire ◽  
Neva C. Durand ◽  
Namita Mitra ◽  
Saul Godinez Pulido ◽  
Ragini Mahajan ◽  
...  
Keyword(s):  
Drug Targets ◽  
De Novo ◽  
Low Cost ◽  
Diagnostic Methods ◽  
Nasopharyngeal Swab ◽  
De Novo Genome Assembly ◽  
Global Pandemic ◽  
Single Person ◽  
Novel Coronavirus ◽  
Almost All

AbstractEarly detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosis of SARS-CoV-2 infection, dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), that enhances sensitivity by aiming to amplify the entire SARS-CoV-2 genome rather than targeting particular viral loci, as in typical RT-PCR assays. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. We are able to reliably (>95% accuracy) detect SARS-CoV-2 at concentrations of 84 genome equivalents per milliliter, better than the reported limits of detection of almost all diagnostic methods currently approved by the US Food and Drug Administration. At higher concentrations, we are able to reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. Such genome assemblies enable the spread of the disease to be analyzed much more effectively than would be possible with an ordinary yes/no diagnostic, and can help identify vaccine and drug targets. Finally, we show that POLAR diagnoses on 10 of 10 clinical nasopharyngeal swab samples (half positive, half negative) match those obtained in a CLIA-certified lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can process 192 samples over the course of an 8-hour experiment, at a cost of ∼$30/patient, enabling a 24-hour turnaround with sequencing and data analysis time included. Further testing and refinement will likely enable greater enhancements in the sensitivity of the above approach.

scholarly journals POS1232 COVID-19 IN PATIENTS WITH SYSTEMIC SCLEROSIS: ONE RHEUMATOLOGY CENTER EXPERIENCE

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 899.2-899
Author(s):  
M. Starovoytova ◽  
O. Desinova ◽  
L. P. Ananyeva ◽  
O. Koneva ◽  
L. Garzanova ◽  
...  
Keyword(s):  
Systemic Sclerosis ◽  
Severe Disease ◽  
High Risk Group ◽  
Nasopharyngeal Swab ◽  
Frequent Use ◽  
Diffuse Form ◽  
Novel Coronavirus ◽  
Almost All ◽  
Dose Prednisone ◽  
Frequent Presence

Background:Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) virus infection or COVID-19 is a serious problem for patients with systemic autoimmune diseases Given the serious complications, including acute lung injury, patients with systemic sclerosis (SSc), especially SSs associated with interstitial lung disease (ILD), may represent a high risk group for infection and the development of severe COVID-19.Objectives:We present an analysis of the COVID-19 course and outcomes in 110 SSc pts.Methods:The study included 147 patients with SSc. The information was clarified by means of telephone survey after 10 months of the pandemic (December 2020). Covid-19 was diagnosed when confirmed by positive oral /nasopharyngeal swab, in the presence of positive antibodies and/or characteristic symptoms, and data from chest computed tomography (CT). 110 pts (77%) out of 147 patients in the SSc registry, gave the necessary information. COVID-19 was diagnosed in 59 pts (53 %). 42 pts (71%) had SSc-ILD. Pts mean age was 54.96 (s.d.11, min 31, max 79), 83% women (49 women and 10 men). 38 pts (65%) had a limited form of SSc, 15 (26%) pts had diffuse form SSc, 6% had overlap (SSc-polymyositis (PM) and SSc had rheumatoid arthritis (RA) and 3% had visceral form of SSc). All patients received low-dose prednisone, and more than half of the pts received immunosuppressive therapy. Rituximab therapy was performed in 24 pts (41%).Results:Almost all patients had positive swab from the oral cavity/nasopharynx. And only in 4 (7%) pts nasopharyngeal swabs were negative, in these patients specific antibodies and characteristic CT changes were detected. Chest CT was performed in 51 (86%) pts. Novel coronavirus pneumonia developed in the vast majority of pts - in 46 (78 %) pts. CT1 (up to 25% of lung lesions) had 10 (17%) pts, CT2 (25-50%) – 21(36%) pts, CT 3 (50-75%) – 15(25%) pts. In 5 (8.5%) pts no changes were detected on CT. The course of COVID-19 was mild and moderate (20 (34%) pts and 18 (31%) pts respectively), severe course was observed in 21 (35%) pts, including fatal in 12 (20%) pts. Among the deceased pts, only 1 patient with SSc-PM had not had ILD, but 7 patients had been treated with rituximab.Conclusion:SSc SARS-CoV-2-infected patients may be at risk of severe disease and mortality due to the frequent presence of ILD and the frequent use of immunosuppressive, including biological, therapy.Disclosure of Interests:None declared

scholarly journals Nanotechnology in Battle against CoViD-19: The Prevention, Diagnosis, and Treatment

2021 ◽  
Vol 10 (4) ◽  
pp. 2637-2645
Keyword(s):  
Detection Methods ◽  
Public Healthcare ◽  
The Novel ◽  
Healthcare Organizations ◽  
Dangerous Situation ◽  
Global Pandemic ◽  
Protection Devices ◽  
The Many ◽  
Novel Coronavirus ◽  
Almost All

People worldwide are experiencing the most dangerous situation concerning the novel severe acute respiratory syndrome known as coronavirus-2 (SARS-CoV-2), commonly referred to as the novel coronavirus disease-2019 (CoViD-19). Since late December 2019, an epidemic of coronavirus disease 2019 (CoViD-19) occurred in Wuhan, China, and rapidly spread to almost all parts of China. With the growing global burden of the CoViD-19 pandemic, scientists, researchers, and healthcare-related organizations constantly work for a viable vaccine or therapeutics, scalable detection methods, personal protection devices, and novel effective medical solutions. Nanotechnology has recently considerably addressed the many clinical and public healthcare issues that have emerged from the CoViD-19 pandemic. The main focus of this current review article is to explore the possibility and potential of nanotechnology to combat this global pandemic and ongoing mitigation techniques and strategies. Furthermore, novel nanotechnology-based products are currently being developed for the prevention, diagnostic, treatment of CoViD-19, which various researchers or healthcare organizations invent.

scholarly journals Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

2019 ◽  
Author(s):  
Zhoutao Chen ◽  
Long Pham ◽  
Tsai-Chin Wu ◽  
Guoya Mo ◽  
Yu Xia ◽  
...  
Keyword(s):  
Long Range ◽  
De Novo ◽  
Low Cost ◽  
Cost Effective ◽  
De Novo Genome Assembly ◽  
Short Read ◽  
Single Tube ◽  
Haplotype Phasing ◽  
A Genome ◽  
Long Read

AbstractLong-range sequencing information is required for haplotype phasing, de novo assembly and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirement. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-Seq™) technology, which enables a low-cost, high-accuracy and high-throughput short-read next generation sequencer to routinely generate over 100 Kb long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcode linked reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate mega-base-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

scholarly journals Barrier for Particle Dispersion Control During Mastoidectomy

2021 ◽  
Author(s):  
Camila Rêgo Muniz ◽  
Carlos Felype Oliveira Pena ◽  
Marcio Ribeiro Studart da Fonseca ◽  
Marcos Rabelo de Freitas
Keyword(s):  
Low Cost ◽  
Particle Dispersion ◽  
World Health ◽  
The Novel ◽  
Surgical Team ◽  
Global Pandemic ◽  
Surgical Field ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Barrier Device

Abstract Introduction The China Health Authority alerted the World Health Organization (WHO) of several cases of pneumonia, and the WHO has declared the novel coronavirus (COVID-19) a global pandemic. Mastoidectomy is a high-risk aerosol generating procedure with the potential to expose the surgeon to infectious particles. Objective Aim to develop a low-cost prototype for a barrier device that can be used during mastoidectomy. Methods Describe the steps involved during otological emergency, requiring immediate surgical procedure, in untested patients. The Otorhinolaryngology Surgical Team of Walter Cantídio Hospital developed the barrier for particle dispersion presented here. Results During surgery, the prototype did not compromise visualization of the surgical field and instrumentation. Microscope repositioning was not compromised or limited by tent Instrumentation and instrument pouch under the Microscope-Tent (MT) performed surgery. After surgery, the plastic sheet was removed simply, without requiring strength. Bone dust and irrigation droplets were collected on the tent. Conclusion Our team developed and practiced, in an otologic emergency, a low-cost and reproducible barrier device that can be used in mastoidectomy in COVID-19 patients. Further tests on efficacy may be necessary.

scholarly journals SARS-CoV-2 detection with de novo designed synthetic riboregulators

2020 ◽  
Author(s):  
Ilkay Cisil Koksaldi ◽  
Recep Erdem Ahan ◽  
Sila Kose ◽  
Nedim Haciosmanoglu ◽  
Ebru Sahin Kehribar ◽  
...  
Keyword(s):  
De Novo ◽  
Point Of Care ◽  
Low Cost ◽  
Critical Role ◽  
World Health ◽  
Global Pandemic ◽  
Health Organization ◽  
Diagnostic Capabilities ◽  
Synthetic Biology Approach

Sars-CoV-2 is a human pathogen and is the main cause of COVID-19 disease. COVID-19 is announced as a global pandemic by World Health Organization. COVID-19 is characterized by severe conditions and early diagnosis can make dramatic changes both for personal and public health. In order to increase the reach for low cost equipment which requires a very limited technical knowledge can be beneficial to diagnose the viral infection. Such diagnostic capabilities can have a very critical role to control the transmission of the disease. Here we are reporting a state-of-the-art diagnostic tool developed by using an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device setting can detect and report presence of Sars-CoV-2 specific genes. The presence of Sars-CoV-2 related genes triggers translation of sfGFP mRNAs, resulting in green fluorescence output. The approach proposed here has the potential of being a game changer in Sars-COV-2 diagnostics by providing an easy-to-run, low-cost-demanding diagnostic capability.

scholarly journals LATE-PCR for LoC Molecular Diagnostics Devices and Its Application to the Sensitive Detection of SARS-CoV-2

2021 ◽  
Vol 6 (1) ◽  
pp. 43
Author(s):  
Dimitrios Karadimas ◽  
George Tsekenis
Keyword(s):  
Point Of Care ◽  
Low Cost ◽  
Diagnostic Testing ◽  
Heat Denaturation ◽  
Nasopharyngeal Swab ◽  
The Novel ◽  
Rt Pcr ◽  
Qualitative Detection ◽  
Novel Coronavirus ◽  
Real Patients

The emergence of the novel coronavirus, SARS-CoV-2, has highlighted the need for rapid, accurate, and point-of-care diagnostic testing. Lab-on-a-Chip (LoC) devices offer the possibility to run such tests at a low cost, while at the same time permitting the multiplexed detection of several viruses when coupled with microarray detection of the amplified products. Herein, we report the development of a protocol for the qualitative detection of SARS-CoV-2, through the design of appropriate primers that target the evolutionary conserved regions of the virus. The proposed protocol relies on an improved version of asymmetric RT-PCR, the linear-after-the-exponential (LATE)-PCR that uses primers that are deliberately designed for use at unequal concentrations. As a result, LATE-PCR exhibits similar efficiency to symmetric PCR, while promoting accumulation of single-stranded products that can subsequently hybridize to a single-strand DNA probe-spotted microarray. The performance of the developed LATE-PCR protocol was compared to that of symmetric RT-PCR, and validated with the use of artificial viral RNA and nasopharyngeal swab samples from real patients. Furthermore, and in order to illustrate its potential for integration into a biosensor platform, the amplicons were allowed to hybridize with probes that were covalently immobilized onto commercially available functionalized glass, without the need for heat denaturation.

scholarly journals DESIGN OF A SMART PREFABRICATED SANITISING CHAMBER FOR COVID-19 USING COMPUTATIONAL FLUID DYNAMICS

2021 ◽  
Vol 27 (2) ◽  
pp. 139-148
Author(s):  
Yousef Abu-Zidan ◽  
Kate Nguyen ◽  
Priyan Mendis ◽  
Sujeeva Setunge ◽  
Hojjat Adeli
Keyword(s):  
Fluid Dynamics ◽  
Computational Fluid Dynamics ◽  
Computer Aided Design ◽  
Close Contact ◽  
Low Cost ◽  
The Novel ◽  
Viral Loads ◽  
Global Pandemic ◽  
Novel Coronavirus ◽  
Aided Design

The novel coronavirus (SARS-CoV-2) has spread at an unprecedented rate, resulting in a global pandemic (COVID-19) that has strained healthcare systems and claimed many lives. Front-line healthcare workers are among the most at risk of contracting and spreading the virus due to close contact with infected patients and settings of high viral loads. To provide these workers with an extra layer of protection, the authors propose a low-cost, prefabricated, and portable sanitising chamber that sprays individuals with sanitising fluid to disinfect clothing and external surfaces on their person. The study discusses computer-aided design of the chamber to improve uniformity of sanitiser deposition and reduce discomfort due to excessive moisture. Advanced computational fluid dynamics is used to simulate the dispersion and deposition of spray particle, and the resulting wetting pattern on the treated person is used to optimise the chamber design.

scholarly journals Pneumocystis jirovecii Pneumonia in a Patient with Lung Adenocarcinoma and EGFR Mutation Treated with Afatinib During the Coronavirus Pandemic 2019

2020 ◽  
pp. 1-3
Author(s):  
Alessandro Morabito ◽  
Agnese Montanino ◽  
Giovanna Esposito ◽  
Giuliano Palumbo ◽  
Anna Manzo ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Cancer Patients ◽  
Pneumocystis Jirovecii ◽  
Empiric Antibiotic Therapy ◽  
Nasopharyngeal Swab ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Global Pandemic ◽  
Empiric Antibiotic ◽  
Infection Disease ◽  
Novel Coronavirus

The novel coronavirus (SARS-CoV-2) or COVID-19 pneumonia is a new global pandemic that can be a challenge for the oncologists. Cancer patients are at high risk of contracting this infection and to develop severe respiratory complications. We present the case of a young patient with a metastatic EGFR positive lung adenocarcinoma in complete remission with afatinib therapy, who developed fever, dyspnea, dry cough, widespread pain and weakness during COVID-19 pandemic in Italy. The thorax computed tomography scan showed suspected pneumonia. Empiric antibiotic therapy was initiated without significant improvement in symptoms. The differential diagnosis included COVID-19 or other pneumonia, mycotic infection, disease progression or afatinib related pneumonia. A SARS-CoV-2 test on a nasopharyngeal swab was repeated twice, and it was negative. Tests for pneumobacteria, cytomegalovirus, tuberculosis bacteria and Legionella were also negative. We further performed a bronchoscopy with bronchoalveolar lavage, and a Pneumocystis jirovecii was microscopically identified. Treatment with trimethoprim-sulfamethoxazole was initiated, with regression of all symptoms. This case confirms the growing difficulties for oncologists during COVID-19 pandemic in the proper management of cancer patients, showing the challenges due to differential diagnoses. In this context, a multidisciplinary approach is crucial to define the best diagnostic and therapeutic strategy.

scholarly journals COVID-19 Detection by Salivary Analysis: Easy and Reliable Approach in Massive Outbreak

2020 ◽  
Vol 5 (1) ◽  
pp. 7
Author(s):  
Dipayan Mojumder ◽  
Satabdi Paul ◽  
Ruman Banik ◽  
Hasina Mahmuda Ferdushi
Keyword(s):  
Body Fluid ◽  
Saliva Sample ◽  
Underlying Mechanism ◽  
Nasopharyngeal Swab ◽  
The World ◽  
Diagnostic Capability ◽  
Targeted Drug ◽  
Novel Coronavirus ◽  
Almost All ◽  
Pcr Test

Coronavirus disease (COVID-19) caused by 2019 Novel Coronavirus (2019-nCoV) recently emerged from Wuhan, Hubei province, China in December 2019. It showed devastating nature and already involved almost all the territories all over the world. It is a contagious disease and rapid, reliable diagnosis is needed to take measure for decreasing the infection rate. For detection of COVID-19 nasopharyngeal swab, sputum, bronchoalveolar lavage, saliva and other body fluid identified as useful samples. The aim of this review from recent studies is to explore the possibility of salivary analysis to identify COVID-19. Although nasopharyngeal swab is taken for rRT-PCR test as a worldwide accepted method, but it is a technique sensitive procedure needs expert personnel and adequate protection is necessary to avoid contamination. In the contrary, saliva sample can be taken easily by the patient himself at home which is a low-risk procedure and economical. So, in the pandemic of COVID-19, salivary analysis could be a good option for detection. Future study on this might explore the possible diagnostic capability of saliva for different diseases and underlying mechanism to find out the pathway for targeted drug therapies.International Journal of Human and Health Sciences Vol. 05 No. 01 January’21 Page: 7-11

scholarly journals A Geroscience Perspective on COVID-19 Mortality

2020 ◽  
Vol 75 (9) ◽  
pp. e30-e33 ◽  
Author(s):  
Daniel E L Promislow
Keyword(s):  
Mortality Rates ◽  
Biological Mechanisms ◽  
Global Pandemic ◽  
Age Dependent ◽  
Causes Of Mortality ◽  
Novel Coronavirus ◽  
Effects Of Aging ◽  
Almost All ◽  
Age And Sex

Abstract A novel coronavirus, SARS-CoV-2, emerged in December 2019, leading within a few months to a global pandemic. COVID-19, the disease caused by this highly contagious virus, can have serious health consequences, though risks of complications are highly age-dependent. Rates of hospitalization and death are less than 0.1% in children, but increase to 10% or more in older people. Moreover, at all ages, men are more likely than women to suffer serious consequences from COVID-19. These patterns are familiar to the geroscience community. The effects of age and sex on mortality rates from COVID-19 mirror the effects of aging on almost all major causes of mortality. These similarities are explored here, and underscore the need to consider the role of basic biological mechanisms of aging on potential treatment and outcomes of COVID-19.

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