scholarly journals COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cristian Tebé ◽  
Joan Valls ◽  
Pau Satorra ◽  
Aurelio Tobías
Keyword(s):  
Data Visualization ◽  
Web Application ◽  
Case Fatality ◽  
Epidemiological Surveillance ◽  
Fatality Rate ◽  
Specific Data ◽  
User Friendly ◽  
And Control ◽  
Shiny Application ◽  
Country Specific

Abstract Background Data analysis and visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance. Results Data on COVID-19 diagnosed cases and mortality, from January 1st, 2020, onwards is collected automatically from the European Centre for Disease Prevention and Control (ECDC). We have developed a Shiny application for data visualization and analysis of several indicators to follow the SARS-CoV-2 epidemic using ECDC data. A country-specific tool for basic epidemiological surveillance, in an interactive and user-friendly manner. The available analyses cover time trends and projections, attack rate, population fatality rate, case fatality rate, and basic reproduction number. Conclusions The COVID19-World online web application systematically produces daily updated country-specific data visualization and analysis of the SARS-CoV-2 epidemic worldwide. The application may help for a better understanding of the SARS-CoV-2 epidemic worldwide.

scholarly journals COVID19-Global: A shiny application to perform a global comparative data visualization for the SARS-CoV-2 epidemic

2020 ◽  
Author(s):  
Aurelio Tobias ◽  
pau satorra ◽  
Joan Valls ◽  
Cristian Tebe
Keyword(s):  
Data Visualization ◽  
Web Application ◽  
Case Fatality ◽  
Global Scale ◽  
Comparative Data ◽  
Epidemiological Surveillance ◽  
Fatality Rate ◽  
Daily Data ◽  
Online Web ◽  
Shiny Application

Data visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance. The COVID19-Global online web application systematically produces daily updated data visualization and analysis of the SARS-CoV-2 epidemic on a global scale. It collects automatically daily data on COVID-19 diagnosed cases and mortality worldwide from January 1st, 2020 onwards. We have implemented comparative data visualization between countries for the most common indicators in epidemiological surveillance to follow an epidemic: attack rate, population fatality rate, case fatality rate, and basic reproduction number. The application may help for a better understanding of the SARS-CoV-2 epidemic worldwide.

scholarly journals COVID19-Tracker: A shiny app to perform comprehensive data visualisation for SARS-CoV-2 epidemic in Spain

2020 ◽  
Author(s):  
Aurelio Tobías ◽  
Joan Valls ◽  
Pau Satorra ◽  
Cristian Tebé
Keyword(s):  
Data Visualization ◽  
Web Application ◽  
Case Fatality Rate ◽  
Reproduction Number ◽  
Case Fatality ◽  
Epidemiological Surveillance ◽  
Data Visualisation ◽  
Short Term ◽  
Daily Data ◽  
Shiny App

AbstractData visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance. The COVID19-Tracker web application systematically produces daily updated data visualization and analysis of the SARS-CoV-2 epidemic in Spain. It collects automatically daily data on COVID-19 diagnosed cases, and mortality from February 24th, 2020 onwards. Several analyses have been developed to visualize data trends and estimating short-term projections; to estimate the case fatality rate; to assess the effect of the lockdown measures on the trends of incident data; to estimate infection time and the basic reproduction number; and to analyse the excess of mortality. The application may help for a better understanding of the SARS-CoV-2 epidemic data in Spain.

scholarly journals XRD Data Visualization, Processing and Analysis with d1Dplot and d2Dplot Software Packages

Proceedings ◽  
2020 ◽  
Vol 62 (1) ◽  
pp. 9
Author(s):  
Oriol Vallcorba ◽  
Jordi Rius
Keyword(s):  
Data Analysis ◽  
Data Visualization ◽  
X Ray Diffraction ◽  
Specific Data ◽  
X Ray ◽  
Software Packages ◽  
Compound Database ◽  
Synchrotron Light ◽  
User Friendly ◽  
Transformation Processes

The d1Dplot and d2Dplot computer programs have been developed as user-friendly tools for the inspection and processing of 1D and 2D X-ray diffraction (XRD) data, respectively. d1Dplot provides general tools for data processing and includes the ability to generate comprehensive 2D plots of multiple patterns to easily follow transformation processes. d2Dplot is a full package for 2D XRD data. Besides general processing tools, it includes specific data analysis routines for the application of the through-the-substrate methodology [Rius et al. IUCrJ 2015, 2, 452–463]. Both programs allow the creation of a user compound database for the identification of crystalline phases. The software can be downloaded from the ALBA Synchrotron Light Source website and can be used free of charge for non-commercial and academic purposes.

scholarly journals COVID-19 in Sudan

2021 ◽  
Vol 15 (02) ◽  
pp. 204-208
Author(s):  
Ayman Ahmed ◽  
Nouh Saad Mohamed ◽  
Sarah Misbah EL-Sadig ◽  
Lamis Ahmed Fahal ◽  
Ziad Bakri Abelrahim ◽  
...  
Keyword(s):  
Health Systems ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Control Measures ◽  
Religious Practices ◽  
Mass Gathering ◽  
Fatality Rate ◽  
High Case Fatality Rate ◽  
The Government ◽  
And Control

The steadily growing COVID-19 pandemic is challenging health systems worldwide including Sudan. In Sudan, the first COVID-19 case was reported on 13th March 2020, and up to 11 November 2020 there were 14,401 confirmed cases of which 9,535 cases recovered and the rest 3,750 cases were under treatment. Additionally, 1,116 deaths were reported, indicating a relatively high case fatality rate of 7.7%. Several preventive and control measures were implemented by the government of Sudan and health partners, including the partial lockdown of the country, promoting social distancing, and suspending mass gathering such as festivals and performing religious practices in groups. However, new cases still emerging every day and this could be attributed to the noncompliance of the individuals to the advocated preventive measurements.

scholarly journals Correlation between immunity from BCG and the morbidity and mortality of COVID-19

2020 ◽  
Author(s):  
Dakshitha Wickramasinghe ◽  
Nilanka Wickramasinghe ◽  
Sohan Anjana Kamburugamuwa ◽  
Carukshi Arambepola ◽  
Dharmabandhu N Samarasekera
Keyword(s):  
Linear Regression Analysis ◽  
Univariate Analysis ◽  
Case Fatality ◽  
Income Level ◽  
Morbidity And Mortality ◽  
Vaccination Policy ◽  
Specific Data ◽  
Bcg Vaccination ◽  
Country Level ◽  
Country Specific

Abstract Background To investigate the association between parameters indicating immunity from BCG at country level (presence of BCG vaccination policy, BCG coverage, age-specific incidence of tuberculosis(TB)) and the morbidity and mortality of COVID-19. Methods Country-specific data for COVID-19 cases and deaths, demographic details, BCG coverage and policy, age-specific TB incidence and income level were obtained. The crude COVID-19 cases and deaths per 100,000 population were calculated and assessed against the parameters indicating immunity from BCG using linear regression analysis. Results Univariate analysis identified higher income level of a country to be significantly associated with COVID-19 cases (p<0.0001) and deaths (p<0.0001) but not with its case fatality rate. The association between COVID-19 and TB was strongest for TB incidence in patients >65-years (Cases(rs=-0.785,p=0.0001)) and deaths (rs=-0.647,p=0.0001).Multivariate analysis identified the higher income level of a country and not having a universal BCG vaccination policy to affect the COVID-19 cases. The deaths were inversely affected by the presence of BCG vaccination policy and coverage; and positively by the TB incidence in patients >65-years. Conclusion Significant inverse correlations observed between cases and deaths of COVID-19 and BCG related parameters highlights immunity from BCG as a likely explanation for the variation in COVID-19 across countries.

scholarly journals The Uncertainties Underlying Herd Immunity against COVID-19

2020 ◽  
Author(s):  
Farid Rahimi ◽  
Amin Talebi Bezmin Abadi
Keyword(s):  
Antiviral Therapy ◽  
Case Fatality Rate ◽  
Herd Immunity ◽  
Case Fatality ◽  
Healthcare Systems ◽  
Fatality Rate ◽  
Economic Implications ◽  
Rate Transmission ◽  
The Social ◽  
And Control

Herd immunity happens when a relatively large proportion of a population becomes infected by an agent, subsequently recovers, and attains immunity against the same agent. That proportion thus indirectly protects the naïve population by preventing the spread of the infection. Herd immunity has been suggested to interrupt and control the COVID-19 pandemic. However, relying on establishing herd immunity can be catastrophic considering the virulence and lethality of SARS-CoV-2. Meanwhile our understanding of the pathogenesis, case-fatality rate, transmission routes, and antiviral therapy for COVID-19 remains limited now. Interrupting or slowing the COVID-19 transmission seems more opportune than vaccination, antiviral therapy, or herd immunity, all of which will take some time to yield. Thus, social distancing, face-masking, and hygiene are the most appropriate immediate countermeasures. Because the social fabrics, economic implications, and local demands of various nations are unique, early relaxation of restrictions may seem hasty particularly when fatality rates are high, or when the healthcare systems could be inadequate or become inundated. Conclusively, avoiding any overwhelmingly risky approach in fighting the pandemic is prudent.

scholarly journals Policy Disparities in Fighting COVID-19 Among Japan, Italy, Singapore and China

2020 ◽  
Author(s):  
Xiaohan Wang ◽  
Leiyu Shi ◽  
Yuyao Zhang ◽  
Haiqian Chen ◽  
Gang Sun
Keyword(s):  
Prevention And Control ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Mitigation Measures ◽  
Cumulative Number ◽  
Fatality Rate ◽  
Epidemic Control ◽  
Growth Trend ◽  
Control Policies ◽  
And Control

Abstract Objective This study systematically summarizes the COVID-19 prevention and control policies of Japan, Italy, China and Singapore in order to provide policy basis for other countries currently coping with the COVID-19 pandemic.Methods This study summarizes the epidemic prevention and control policies in Japan, Italy, China, and Singapore, and analyzes the effects of policies in the four countries using official statistics.Results As of May 27, 2020, the growth trend of new cases in Japan, Italy, China and Singapore has all stabilized. However, the cumulative number of confirmed cases (231139) and case-fatality rate (14.3%) in Italy far exceeded those in the other three countries, and the effect of epidemic control was inferior. Singapore began to experience a domestic resurgence after April 5, with a cumulative number of confirmed cases reaching 32876, but the case-fatality rate remained extremely low (0.1%). The growth of cumulative confirmed cases in China (84547) is almost stagnant, and the case-fatality rate is low (5.5%). The growth of cumulative confirmed cases in Japan (16661) increased slowly, and the case-fatality rate (4.8%) was slightly lower than that in China.Conclusion This study divides the epidemic prevention and control policies of the four countries into two categories: the blocking measures taken by China and Singapore, and the mitigation measures taken by Japan and Italy. According to the results of epidemic control in the four countries, we can conclude that the blocking measures are more effective. Pay attention to the admission of mild patients and cases tracking as the core strategy of blocking measures, which can be considered in countries all over the world.

scholarly journals Egypt's COVID-19 Recent Happenings and Perspectives: A Mini-Review

2021 ◽  
Vol 9 ◽  
Author(s):  
AbdulRahman A. Saied ◽  
Asmaa A. Metwally ◽  
Norah Abdullah Bazekh Madkhali ◽  
Shafiul Haque ◽  
Kuldeep Dhama
Keyword(s):  
Case Fatality Rate ◽  
Case Fatality ◽  
Animal Origin ◽  
Fatality Rate ◽  
Health Concerns ◽  
The World ◽  
The Usa ◽  
Egyptian Government ◽  
Low Prevalence ◽  
And Control

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected countries across the world. While the zoonotic aspects of SARS-CoV-2 are still under investigation, bats and pangolins are currently cited as the animal origin of the virus. Several types of vaccines against COVID-19 have been developed and are being used in vaccination drives across the world. A number of countries are experiencing second and third waves of the pandemic, which have claimed nearly four million lives out of the 180 million people infected globally as of June 2021. The emerging SARS-CoV-2 variants and mutants are posing high public health concerns owing to their rapid transmissibility, higher severity, and in some cases, ability to infect vaccinated people (vaccine breakthrough). Here in this mini-review, we specifically looked at the efforts and actions of the Egyptian government to slow down and control the spread of COVID-19. We also review the COVID-19 statistics in Egypt and the possible reasons behind the low prevalence and high case fatality rate (CFR%), comparing Egypt COVID-19 statistics with China (the epicenter of COVID-19 pandemic) and the USA, Brazil, India, Italy, and France (the first countries in which the numbers of patients infected with COVID-19). Additionally, we have summarized the SARS-CoV-2 variants, vaccines used in Egypt, and the use of medicinal plants as preventive and curative options.

scholarly journals Another vision of the situation of the COVID-19 pandemic in Mexico during 2020

2021 ◽  
pp. 1-9
Author(s):  
Sergio Isaac De La Cruz Hernández
Keyword(s):  
Health System ◽  
Case Fatality Rate ◽  
Public Health System ◽  
Case Fatality ◽  
Sentinel Surveillance ◽  
Epidemiological Surveillance ◽  
Fatality Rate ◽  
The Public ◽  
Mexican Government ◽  
High Positivity Rate

Abstract The number of coronavirus disease 2019 (COVID-19) cases and deaths registered in Mexico during 2020 could be underestimated, due to the sentinel surveillance adopted in this country. Some consequences of following this type of epidemiological surveillance were the high case fatality rate and the high positivity rate for COVID-19 shown in Mexico in 2020. During this year, the Mexican Ministry of Health only considered cases from the public health system, which followed this sentinel surveillance, but did not consider those cases from the private health system. To better understand this pandemic, it is important to include all the results obtained by all the institutions capable of testing for COVID-19, thus the Mexican Government could make good decisions to protect the population from this disease.

scholarly journals A new method to calculate the instant case fatality rate of COVID-19 in Wuhan and Hubei of China

2020 ◽  
Author(s):  
Lei Cao ◽  
Ting-ting Huang ◽  
Jun-xia Zhang ◽  
Qi Qin ◽  
Si-yu Liu ◽  
...  
Keyword(s):  
Case Fatality Rate ◽  
Large Deviation ◽  
Case Fatality ◽  
Mortality Rates ◽  
Fatality Rate ◽  
Cure Rate ◽  
Wuhan City ◽  
Notification Data ◽  
And Control ◽  
Case Notification

Abstract The worst-hit area of coronavirus disease 2019 (COVID-19) in China was Wuhan City and its affiliated Hubei Province, where the outbreak has been well controlled. The case fatality rate (CFR) is the most direct indicator to evaluate the hazards of an infectious disease. However, most reported CFR on COVID-19 represent a large deviation from reality. We aimed to establish a more accurate way to estimate the CFR of COVID-19 in Wuhan and Hubei and compare it to the reality. The daily case notification data of COVID-19 from December 8, 2019, to May 1, 2020, in Wuhan and Hubei were collected from the bulletin of the Chinese authorities. The instant CFR of COVID-19 was calculated from the numbers of deaths and the number of cured cases, the two numbers occurred on the same estimated diagnosis dates. The instant CFR of COVID-19 was 1.3%-9.4% in Wuhan and 1.2%-7.4% in Hubei from January 1 to May 1, 2020. It has stabilized at 7.69% in Wuhan and 6.62% in Hubei since early April. The cure rate was between 90.1% and 98.8% and finally stabilized at 92.3% in Wuhan and stabilized at 93.5% in Hubei. The mortality rates were 34.5/100 000 in Wuhan and 7.61/100 000 in Hubei. In conclusion, this approach reveals a way to accurately calculate the CFR, which may provide a basis for the prevention and control of infectious diseases.

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