scholarly journals SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes

2021 ◽  
Author(s):  
Ryota Shimada ◽  
Emily N. Alden ◽  
Kendall Hoff ◽  
Dun Ding ◽  
Jiayi Sun ◽  
...  
Keyword(s):  
Moving Average ◽  
Tiling Array ◽  
Cost Effective ◽  
The Novel ◽  
Cost Effective Method ◽  
A Genome ◽  
Novel Coronavirus ◽  
Average Filter ◽  
Genome Tiling Array ◽  
Variant Identification

With over three million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. We previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome when compared to traditional short read sequencing methods which can be time consuming and costly. Herein we present the addition of genotyping probes to our DNA chip which target known SARS-CoV-2 variants. The incorporation of the genotyping probe sets along with the advent of a moving average filter have improved our sequencing coverage and accuracy of the SARS-CoV-2 genome.

scholarly journals When Second Best Might be the Best: Using Hospitalization Data to Monitor the Novel Coronavirus Pandemic

2020 ◽  
Author(s):  
Peter J Mallow ◽  
Michael Jones
Keyword(s):  
Moving Average ◽  
Hospital Utilization ◽  
High Rate ◽  
Ideal Solution ◽  
The Novel ◽  
Policy Makers ◽  
Hospital Administrators ◽  
Utilization Data ◽  
Novel Coronavirus ◽  
The Ideal

The novel coronavirus' high rate of asymptomatic transmission combined with a lack of testing kits call for a different approach to monitor its spread and severity. We proposed the use of hospitalizations and hospital utilization data to monitor the spread and severity. A proposed threshold of a declining 7-day moving average over a 14-day period, "7&14" was set to communicate when a wave of the novel coronavirus may have passed. The state of Ohio was chosen to illustrate this threshold. While not the ideal solution for monitoring the spread of the epidemic, the proposed approach is an easy to implement framework accounting for limitations of the data inherent in the current epidemic. Hospital administrators and policy makers may benefit from incorporating this approach into their decision making.

scholarly journals A Simple, Efficient, and Eco-Friendly Method for the Preparation of 3-Substituted-2,3-dihydroquinazolin-4(1H)-one Derivatives

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4052 ◽  
Author(s):  
Zainab Almarhoon ◽  
Kholood A. Dahlous ◽  
Rakia Abd Alhameed ◽  
Hazem A. Ghabbour ◽  
Ayman El-Faham
Keyword(s):  
Molecular Structure ◽  
Cost Effective ◽  
Environmentally Benign ◽  
Conventional Heating ◽  
Second Step ◽  
The Novel ◽  
Monoclinic Crystal ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cost Effective Method

A simple, cost-effective method under environmentally benign conditions is a very important concept for the preparation of 2,3-dihydroquinazolin-4(1H)-one derivatives. The present work describes an efficient and eco-friendly protocol for the synthesis of 2-amino-N-(2-substituted-ethyl)benzamide and 3-substituted-2,3-dihydroquinazolin-4(1H)-one derivatives. The novel feature of this protocol is the use of 2-methyl tetrahydrofuran (2-MeTHF) as an eco-friendly alternative solvent to tetrahydrofuran (THF) in the first step. In the second step, methanol in the presence of potassium carbonate as a catalyst was used under conventional heating or microwave irradiation, which provided an eco-friendly method to afford the target products in excellent yields and purities. NMR (1H and 13C), elemental analysis, and LC-MS confirmed the structures of all compounds. X-ray crystallography further confirmed the structure of the intermediate 2-amino-N-(2-substituted-ethyl)benzamide 3a. The molecular structure of 3a was monoclinic crystal, with P21/c, a = 13.6879 (11) Å, b = 10.2118 (9) Å, c = 9.7884 (9) Å, β = 105.068 (7)°, V = 1321.2 (2) Å3, and Z = 4.

scholarly journals Enhancement of the Comb Filtering Selectivity Using Iterative Moving Average for Periodic Waveform and Harmonic Elimination

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
José L. Ferreira ◽  
Yan Wu ◽  
Ronald M. Aarts
Keyword(s):  
Moving Average ◽  
Spectral Lines ◽  
Comb Filter ◽  
The Novel ◽  
Harmonic Elimination ◽  
Novel Method ◽  
Eeg Recordings ◽  
Notch Filtering ◽  
Iterative Filtering ◽  
Average Filter

A recurring problem regarding the use of conventional comb filter approaches for elimination of periodic waveforms is the degree of selectivity achieved by the filtering process. Some applications, such as the gradient artefact correction in EEG recordings during coregistered EEG-fMRI, require a highly selective comb filtering that provides effective attenuation in the stopbands and gain close to unity in the pass-bands. In this paper, we present a novel comb filtering implementation whereby the iterative filtering application of FIR moving average-based approaches is exploited in order to enhance the comb filtering selectivity. Our results indicate that the proposed approach can be used to effectively approximate the FIR moving average filter characteristics to those of an ideal filter. A cascaded implementation using the proposed approach shows to further increase the attenuation in the filter stopbands. Moreover, broadening of the bandwidth of the comb filtering stopbands around −3 dB according to the fundamental frequency of the stopband can be achieved by the novel method, which constitutes an important characteristic to account for broadening of the harmonic gradient artefact spectral lines. In parallel, the proposed filtering implementation can also be used to design a novel notch filtering approach with enhanced selectivity as well.

scholarly journals A Simple Colorimetric Molecular Detection of Novel Coronavirus (COVID-19), an Essential Diagnostic Tool for Pandemic Screening

2020 ◽  
Author(s):  
Pazhanimuthu Annamalai ◽  
Madhu Kanta ◽  
Pazhanivel Ramu ◽  
Baskar Ravi ◽  
Kokilavani Veerapandian ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Point Of Care ◽  
Lamp Assay ◽  
High Sensitivity ◽  
Cost Effective ◽  
Cost Effective Method ◽  
Recent Outbreak ◽  
Pcr Method ◽  
Novel Coronavirus ◽  
Virus Isolates

AbstractThe recent outbreak of the newly emerged novel coronavirus (SARS-CoV-2) presents a big challenge for public health laboratories as virus isolates are not available while there is an increasing evidence that the epidemic is more widespread than initially thought, as well as spreading internationally across borders through travellers does already happen warranting a methodology for the rapid detection of the infection to control SARS-CoV-2. Aim: We intended to develop and deploy a robust and rapid diagnostic methodology using LAMP assay for use in point of care settings to detect SARS-COV-2 infection. Methodology: In the present study, we have developed a validated rapid diagnostic procedure to detect SARS-CoV-2 using LAMP assay, its design relying on isothermal amplification of the nucleic acids of the SARS-CoV-2. Results: The LAMP assay developed detects SARS-CoV-2 infection rapidly with high sensitivity and reliability. The data generated by LAMP assay were comparable and at par with the data generated by real-time PCR method. Conclusion: The present study demonstrates that the LAMP assay developed was a rapid, reliable, sensitive and cost effective method to detect SARS-CoV-2 infection in a point of care as well as in laboratory settings.

scholarly journals Mathematical modelling and optimal cost-effective control of COVID-19 transmission dynamics

2020 ◽  
Author(s):  
S. Olaniyi ◽  
O.S. Obabiyi ◽  
K.O. Okosun ◽  
A.T. Oladipo ◽  
S.O. Adewale
Keyword(s):  
Basic Reproduction Number ◽  
Least Squares Method ◽  
Reproduction Number ◽  
Cost Effective ◽  
Effective Control ◽  
Cumulative Number ◽  
The Novel ◽  
Novel Coronavirus ◽  
Disease Free ◽  
The Basic Reproduction Number

Abstract The novel coronavirus disease (COVID-19) caused by a new strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains the current global health challenge. In this paper, an epidemic model based on system of ordinary differential equations is formulated by taking into account the transmission routes from symptomatic, asymptomatic and hospitalized individuals. The model is fitted to the corresponding cumulative number of hospitalized individuals (active cases) reported by the Nigeria Centre for Disease Control (NCDC), and parameterized using the least squares method. The basic reproduction number which measures the potential spread of COVID-19 in the population is computed using the next generation operator method. Further, Lyapunov function is constructed to investigate the stability of the model around a disease-free equilibrium point. It is shown that the model has a globally asymptotically stable disease-free equilibrium if the basic reproduction number of the novel coronavirus transmission is less than one. Sensitivities of the model to changes in parameters are explored. It is revealed further that the basic reproduction number can be brought to a value less than one in Nigeria, if the current effective transmission rate of the disease can be reduced by 50%. Otherwise, the number of active cases may get up to 2.5% of the total estimated population. In addition, two time-dependent control variables, namely preventive and management measures, are considered to mitigate the damaging effects of the disease using Pontryagin's maximum principle. The most cost-effective control measure is determined through cost-effectiveness analysis. Numerical simulations of the overall system are implemented in MatLab® for demonstration of the theoretical results.

scholarly journals A model for survival rate projection of Covid19 patients

2020 ◽  
Author(s):  
Devika P. Madalli ◽  
Sagar Bhimrao Gajbe ◽  
Gopalji ◽  
Akhilesh Ajith Kumar
Keyword(s):  
Survival Rate ◽  
Error Rate ◽  
Death Rate ◽  
Moving Average ◽  
The Novel ◽  
Active Infection ◽  
Learning Module ◽  
The World ◽  
Projection Error ◽  
Novel Coronavirus

Abstract The novel coronavirus has been declared a worldwide pandemic. The pandemic has unleashed health as well as economic devastation across the world. In view of this, various governments, researchers and agencies are trying to work towards solutions to control the spread of the virus. There are many studies that have been initiated that consider the various parameters that contribute to the spread of the virus. We present a model to predict the survival rate of Covid19 infected patients. The study takes into consideration death rate (normal) and Covid infection death rate in India. Other factors considered are the number of infections and active infection numbers. We also incorporate a ‘learning module’ to learn from the observed error rate. We compute the moving average of error which is then deployed to minimise projection error in the model. The factor obtained from the learning is deployed into the survival rate computation to achieve best results.

scholarly journals Convalescent Blood: Current Perspective on the Efficacy of a Legacy Approach in COVID-19 Treatment

2021 ◽  
pp. 1-14
Author(s):  
Roghayeh Sheervalilou ◽  
Milad Shirvaliloo ◽  
Saman Sargazi ◽  
Soraiya Bahari ◽  
Ramin Saravani ◽  
...  
Keyword(s):  
Blood Transfusion ◽  
Unknown Origin ◽  
Cost Effective ◽  
Viral Disease ◽  
The Novel ◽  
New Approach ◽  
Current Perspective ◽  
Antiviral Medication ◽  
Novel Coronavirus ◽  
Almost All

Since early 2020, COVID-19 has wreaked havoc in many societies around the world. As of the present, the SARS-CoV-2-borne disease is propagating in almost all countries, affecting hundreds of thousands of people in an unprecedented way. As the name suggests, the novel coronavirus, widely known as SARS-CoV-2, is a new emerging human pathogen. A novel disease of relatively unknown origin, COVID-19 does not seem to be amenable to the currently available medicines since there is no specific cure for the disease. In the absence of any vaccine or effective antiviral medication, we have no tools at our disposal, but the method of quarantine, be it domestic or institutional, to hinder any further progression of this outbreak. However, there is a record of physicians in the past who practiced convalescent blood transfusion. To their awe, the method seemed to be useful. It is anticipated that these contemporary methods will outdo any other vaccination process in the time being, as blood transfusion is instead a cost-effective and time-friendly technique. Following a successful trial, this new approach of contemporary nature to a viral disease may serve as an emergency intervention to intercept infectious outbreaks and prevent an impending epidemic/pandemic. In this review, we document the most recent evidence regarding the efficiency of convalescent plasma and serum therapy on SARS, MERS, and particularly COVID-19, while discussing potential advantages and possible risks of such practice.

scholarly journals A model for survival rate projection of Covid19 patients

2020 ◽  
Author(s):  
Devika P. Madalli ◽  
Sagar Bhimrao Gajbe ◽  
Gopalji ◽  
Akhilesh Ajith Kumar
Keyword(s):  
Survival Rate ◽  
Error Rate ◽  
Death Rate ◽  
Moving Average ◽  
The Novel ◽  
Active Infection ◽  
Learning Module ◽  
The World ◽  
Projection Error ◽  
Novel Coronavirus

Abstract The novel coronavirus has been declared a worldwide pandemic. The pandemic has unleashed health as well as economic devastation across the world. In view of this, various governments, researchers and agencies are trying to work towards solutions to control the spread of the virus. There are many studies that have been initiated that consider the various parameters that contribute to the spread of the virus. We present a model to predict the survival rate of Covid19 infected patients. The study takes into consideration death rate (normal) and Covid infection death rate in India. Other factors considered are the number of infections and active infection numbers. We also incorporate a ‘learning module’ to learn from the observed error rate. We compute the moving average of error which is then deployed to minimise projection error in the model. The factor obtained from the learning is deployed into the survival rate computation to achieve best results.

scholarly journals The Impact of the Lockdown Measure on the Confirmed Cases of the Novel Coronavirus (COVID-19) in Nigeria

2020 ◽  
pp. 110-119
Author(s):  
Charles Okechukwu Aronu ◽  
Nkechi Udochukwu Otty ◽  
Jacob Chinedum Ehiwario ◽  
Patrick Nnaemeka Okafor
Keyword(s):  
West Africa ◽  
Moving Average ◽  
Arima Model ◽  
Secondary Data ◽  
The Novel ◽  
Test Analysis ◽  
Significant Difference ◽  
Daily Report ◽  
Novel Coronavirus ◽  
The Impact

Aims: This study examined the impact of the lockdown measure on the confirmed cases of the Novel Coronavirus (COVID-19) in Nigeria.  The objectives of the study include to identifying an appropriate autoregressive integrated moving average (ARIMA) model that is adequate for estimating the reported cases of COVID-19 in Nigeria and to ascertain whether the ease of lockdown has a significant impact on the reported cases of COVID-19 in Nigeria.  Place and Duration of Study: The source of the data used for this study was the secondary data obtained from the daily report of the United Nations Office for the Coordination of Humanitarian Affairs (OCHA) from 1st February 2020 to 30th June 2020. Methodology: The statistical tools used for data analysis are the ARIMA time series model and the Chow test analysis. Results: Nigeria ranked 1st in West Africa sub-region with a total of 25, 133 confirmed COVID-19 cases, followed by Ghana with 17, 351 confirmed cases while Gambia recorded the least number of confirmed cases with 47 cases of COVID19. The ARIMA (0, 1, 1) was identified as the best model for forecasting the confirmed COVID-19 cases in Nigeria within the observed period. It was found that there exists a significant difference in the number of confirmed cases of COVID-19 during the lockdown period and the post lockdown period. Conclusion: The study revealed that Nigeria has the most confirmed cases of COVID-19 in West Africa region. Also, the ease of the lockdown was found to increase the number of confirmed virus cases in Nigeria.

The Effect of Hydroxychloroquine on Mortality and Pneumonia Development in SARS-Cov-2 Positive Mildly Symptomatic Outpatients without Findings of Pneumonia

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Kara A ◽  
◽  
Guner R ◽  
Erdinç S ◽  
Korukoglu G ◽  
...  
Keyword(s):  
Risk Group ◽  
Health Information System ◽  
Early Period ◽  
Cost Effective ◽  
Underlying Disease ◽  
The Novel ◽  
Shortness Of Breath ◽  
Early Use ◽  
Lung Auscultation ◽  
Novel Coronavirus

Although a period longer than 10 months has passed since the detection of the first cases in and more than 40 million people have been diagnosed with COVID-19 worldwide, there is still no well-accepted and proven treatment choice for the novel coronavirus disease. This study aimed to retrospectively investigate cases in whom treatment had started due to detected as positive during screening and also having shown signs including fever, cough, shortness of breath, excessive malaise, fatigue or loss of smell-taste, without any findings of pneumonia between March 11, 2020, when the first cases were detected in Turkey, and the beginning of May, 2020. A total of 19.276 SARS-CoV-2 PCR positive outpatients, within the first 48 hours of detection and had no findings in lung auscultation or radiology, were detected from the data of Health Information System. 9559 patients were males (49.6%) and 9717 were females (50.4%). An underlying disease considered in the risk group for COVID-19 was found in 1789 of the patients (8.8%). An underlying disease was present in 9.4% using hydroxychloroquine and in 9% not using hydroxychloroquine. 43 deaths (0.2%) were detected among all cases. Mortality in cases using and not using hydroxychloroquine was respectively 5 (in 12.293 cases) and 38 (in 6.983 cases). It was confirmed that pneumonia developed in 2.080 of the patients (10.8%). This number was found as 1286 (10.5%) in cases using HQ and as 794 (11.4%) in cases not using HQ. In conclusion, since this study confirmed that hydroxychloroquine used in outpatients presenting in the early period without any symptoms of pneumonia can ensure survival and prevent pneumonia development particularly in young adults, we may speculate that the early use of hydroxychloroquine in mildly symptomatic patients results in a cost-effective and potent treatment.

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