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

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.

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

BMC Medical Research Methodology ◽

10.1186/s12874-020-01121-9 ◽

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.

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

10.1101/2020.04.01.20049684 ◽

2020 ◽

Cited By ~ 3

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.

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

Disaster Medicine and Public Health Preparedness ◽

10.1017/dmp.2021.340 ◽

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.

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Dengue Infections in Colombia: Epidemiological Trends of a Hyperendemic Country

Tropical Medicine and Infectious Disease ◽

10.3390/tropicalmed5040156 ◽

2020 ◽

Vol 5 (4) ◽

pp. 156

Author(s):

Hernando Gutierrez-Barbosa ◽

Sandra Medina-Moreno ◽

Juan C. Zapata ◽

Joel V. Chua

Keyword(s):

Public Health ◽

Case Fatality ◽

Public Health Problem ◽

Epidemiological Surveillance ◽

Severe Dengue ◽

Major Public Health Problem ◽

Seasonal Temperature ◽

Fatality Rate ◽

Notification Rate ◽

Epidemiological Trends

Dengue is a major public health problem in hyperendemic countries like Colombia, the understanding of the epidemiological trends is important for the development of efficient public health policies. We conducted a systematic review of the epidemiologic data on dengue in Colombia from 1971 to 2020. A total of 375 relevant citations were identified, 36 of which fulfilled the inclusion criteria. The data of dengue and severe dengue cases, infection fatality rate, and serotype distribution were used to understand and identify gaps in the epidemiological knowledge in Colombia. The epidemiology of dengue in this country was characterized by five main outbreaks in 1998, 2002, 2010, 2013, and 2019 with high fatality rates in comparison with the average values reported in the Americas. The case fatality rate of severe dengue exceeded 2% and all four serotypes co-circulate throughout the country with some regional variations. Overall, the behavior of dengue in Colombia is influenced by multiple factors including seasonal temperature variation and socioeconomic conditions. Additionally, the most important barriers in the epidemiological surveillance of dengue may be due to the insufficient notification rate in some regions and the low active search for the circulation of different serotypes.

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The increase in the risk of severity and fatality rate of covid-19 in southern Brazil after the emergence of the Variant of Concern (VOC) SARS-CoV-2 P.1 was greater among young adults without pre-existing risk conditions

10.1101/2021.04.13.21255281 ◽

2021 ◽

Author(s):

André Ricardo Ribas Freitas ◽

Daniele Rocha Queiróz Lemos ◽

Otto Albuquerque Beckedorff ◽

Luciano Pamplona de Góes Cavalcanti ◽

Andre M Siqueira ◽

...

Keyword(s):

Age Groups ◽

Case Fatality ◽

The State ◽

Epidemiological Surveillance ◽

Fatality Rate ◽

Risk Of Death ◽

New Variant ◽

Before And After ◽

Almost All ◽

Second Wave

ABSTRACTBackgroundThe SARS-CoV-2 P.1 variant has been considered as “variant of concern (VOC)” since the end of 2020 when it was firstly identified in the Brazilian state of Amazonas and from there spread to other regions of Brazil. This variant was associated with an increase in transmissibility and worsening of the epidemiological situation in the places where it was detected. The aim of this study was to analyze the severity profile of covid-19 cases in the Rio Grande do Sul state, southern region of Brazil, before and after the emergence of the P.1 variant, considering also the context of the hospitals overload and the collapse of health services.MethodsWe analyzed data from the Influenza Epidemiological Surveillance Information System, SIVEP-Gripe (Sistema de Informação de Vigilância Epidemiológica da Gripe) and compare two epidemiological periods: the “first wave” comprised by cases occurred during November and December 2020 (EW 45 to 53) and the “second wave” with cases occurred in February 2021 (EW 5 to 8), considering that in this month there was a predominance of the new variant P.1. We calculated the proportion of severe forms among the total cases of covid-19, the case fatality rates (CFR) and hospital case fatality rate (hCFR) over both waves time set using the date of onset of symptoms as a reference. We analyzed separately the patients without pre-existing conditions of risk, by age and sex. For comparison between periods, we calculated the Risk Ratio (RR) with their respective 95% confidence intervals and the p-values.FindingsWe observed that in the second wave there were an increase in the proportion of severe cases and covid-19 deaths among younger age groups and patients without pre-existing conditions of risk. The proportion of people under the age of 60 among the cases that evolved to death raised from 18% (670 deaths) in November and December (1st wave) to 28% (1370 deaths) in February (2nd wave). A higher proportion of patients without pre-existing risk conditions was also observed among those who evolved to death due to covid-19 in the second wave (22%, 1,077 deaths) than in the first one (13%, 489 deaths). The CFR for covid-19 increased overall and in different age groups, in both sexes. The increase occurred in a greatest intensity in the population between 20 and 59 years old and among patients without pre-existing risk conditions. Female 20 to 39 years old, with no pre-existing risk conditions, were at risk of death 5.65 times higher in February (95%CI = 2.9 - 11.03; p <0.0001) and in the age group of 40 and 59 years old, this risk was 7.7 times higher (95%CI = 5.01-11.83; p <0.0001) comparing with November-December.InterpretationOur findings showed an increase in the proportion of young people and people without previous illnesses among severe cases and deaths in the state of RS after the identification of the local transmission of variant P.1 in the state. There was also an increase in the proportion of severe cases and in the CFR, in almost all subgroups analyzed, this increase was heterogeneous in different age groups and sex. As far as we know, these are the first evidences that the P.1 variant can disproportionately increase the risk of severity and deaths among population without pre-existing diseases, suggesting related changes in pathogenicity and virulence profiles. New studies still need to be done to confirm and deepen these findings.

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Hospitalizations related to meningococcal infection in Spain from 1997 to 2018

BMC Infectious Diseases ◽

10.1186/s12879-021-06916-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Stefan Walter ◽

Ruth Gil-Prieto ◽

Mario Gil-Conesa ◽

Gil Rodriguez-Caravaca ◽

Jesús San Román ◽

...

Keyword(s):

Case Fatality Rate ◽

Age Groups ◽

Case Fatality ◽

Hospitalization Rate ◽

Epidemiological Surveillance ◽

Meningococcal Infection ◽

Fatality Rate ◽

Hospitalization Rates ◽

Diagnostic Position ◽

Children Under 5

Abstract Background Baseline hospitalization, mortality, and in-hospital fatality rates for meningococcal infection are required to evaluate preventive interventions, such as the inclusion of the conjugated quadrivalent meningococcal vaccine and serogroup B based protein vaccines. Methods All meningococcal infection–related hospitalizations in any diagnostic position in Spain from 1st January 1997 through 31st December 2018 were analysed. The annual hospitalization rate, mortality rate and case-fatality rate were calculated. Results The average hospitalization rate for meningococcal infection was 1.64 (95% CI 1.61 to 1.66) hospitalizations per 100,000 inhabitants during the study period and significantly decreased from 1997 to 2018. Hospitalizations for meningococcal infection decreased significantly with age and were concentrated in children under 5 years of age (46%). The hospitalization rates reached 29 per 100,000 and 24 per 100,000 children under 1 and 2 years of age, respectively. The in-hospital case-fatality rate was 7.45% (95% CI 7.03 to 7.86). Thirty percent of the deaths occurred in children under 5 years of age, and more than half occurred in adults. The case fatality rate increased significantly with age (p < 0.001). Conclusion It is necessary to maintain epidemiological surveillance of meningococcal infection to determine the main circulating serogroups involved, track their evolution, and evaluate preventive measures whose effectiveness must be assessed in all age groups.

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AUTOMAP: solution for geospatial monitoring in public health

10.31234/osf.io/xargu ◽

2021 ◽

Author(s):

Nelly Lopes de Moraes Gil ◽

Aline Chotte de Oliveira ◽

Gabriela Ganassin ◽

Carolina Luca ◽

Sandra Pelloso ◽

...

Keyword(s):

Public Health ◽

Real Time ◽

Web Application ◽

Decision Makers ◽

Health Conditions ◽

Epidemiological Surveillance ◽

Free Access ◽

Evidence Based ◽

Health Decision ◽

Shiny Application

Background: Health decision-makers currently face the challenge of accumulating health data in time to inform evidence-based interventions to improve health outcomes. The Brazilian healthcare system is in need of daily primary care data reported in real-time to support evidence-based policy decisions. This study aims to detail the development of a solution for geospatial monitoring in public health called AUTOMAP. Its main objective is to facilitate epidemiological surveillance and promote that rapidly available data improve the provision of health services. Methods: AUTOMAP is an application that articulates concepts inherent to epidemiological surveillance, geographic information systems, and free access technologies to design a monitoring tool of health conditions. The system architecture consists of three modules: user, application, and database. They work together to collect information regarding health conditions, its processing, and dynamic viewing. AUTOMAP design uses the statistical language R, which employs literate programming through a Shiny application package to transform statistical results of health conditions into interactive maps in real-time. AUTOMAP is a web application that has two interfaces: one for loading data and another for generating dynamic epidemiological maps. Conclusion: AUTOMAP allows a variety of clinical solutions, such as risk calculators, spatial evaluation of events of interest, decision models, simulations, and epidemiological patient monitoring. The software is open-source with easy accessibility, allowing anyone to make adjustments and handle a myriad of health conditions, thus being applicable globally. AUTOMAP is a tool that will facilitate and advance data collection for evidence generation and expedite evidence-based health system improvements.

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Preliminary Estimate of COVID-19 Case Fatality Rate in the Philippines using Linear Regression Analysis

SSRN Electronic Journal ◽

10.2139/ssrn.3569248 ◽

2020 ◽

Author(s):

Michael Arieh Medina

Keyword(s):

Regression Analysis ◽

Linear Regression ◽

Case Fatality Rate ◽

Linear Regression Analysis ◽

Case Fatality ◽

The Philippines ◽

Fatality Rate ◽

Preliminary Estimate

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Impact of hydroxychloroquin/azithromycin protocol on COVID-19 case-fatality rate reduction in Algeria. (Preprint)

10.2196/preprints.20886 ◽

2020 ◽

Author(s):

Ahmed Youssef Kada

Keyword(s):

Case Fatality Rate ◽

Doubling Time ◽

Case Fatality ◽

World Health ◽

Fatality Rate ◽

Therapeutic Protocol ◽

First Case ◽

The World ◽

The Impact ◽

At Home

BACKGROUND Covid-19 is an emerging infectious disease like viral zoonosis caused by new coronavirus SARS CoV 2. On December 31, 2019, Wuhan Municipal Health Commission in Hubei province (China) reported cases of pneumonia, the origin of which is a new coronavirus. Rapidly extendable around the world, the World Health Organization (WHO) declares it pandemic on March 11, 2020. This pandemic reaches Algeria on February 25, 2020, date on which the Algerian minister of health, announced the first case of Covid-19, a foreign citizen. From March 1, a cluster is formed in Blida and becomes the epicentre of the coronavirus epidemic in Algeria, its total quarantine is established on March 24, 2020, it will be smoothly alleviated on April 24. A therapeutic protocol based on hydroxychloroquine and azithromycin was put in place on March 23, for complicated cases, it was extended to all the cases confirmed on April 06. OBJECTIVE This study aimed to demonstrate the effectiveness of hydroxychloroquin/azithromycin protocol in Algeria, in particular after its extension to all patients diagnosed COVID-19 positive on RT-PCR test. We were able to illustrate this fact graphically, but not to prove it statistically because the design of our study, indeed in the 7 days which followed generalization of therapeutic protocol, case fatality rate decrease and doubling time increase, thus confirming the impact of wide and early prescription of hydroxychloroquin/azithromycin protocol. METHODS We have analyzed the data collected from press releases and follow-ups published daily by the Ministry of Health, we have studied the possible correlations of these data with certain events or decisions having a possible impact on their development, such as confinement at home and its reduction, the prescription of hydroxychloroquine/azithromycin combination for serious patients and its extension to all positive COVID subjects. Results are presented in graphics, the data collection was closed on 31/05/2020. RESULTS Covid-19 pandemic spreads from February 25, 2020, when a foreign citizen is tested positive, on March 1 a cluster is formed in the city of Blida where sixteen members of the same family are infected during a wedding party. Wilaya of Blida becomes the epicentre of coronavirus epidemic in Algeria and lockdown measures taken, while the number of national cases diagnosed begins to increases In any event, the association of early containment measures combined with a generalized initial treatment for all positive cases, whatever their degree of severity, will have contributed to a reduction in the fatality rate of COVID 19 and a slowing down of its doubling time. CONCLUSIONS In Algeria, the rapid combination of rigorous containment measure at home and early generalized treatment with hydroxychloroquin have demonstrated their effectiveness in terms of morbidity and mortality, the classic measures of social distancing and hygiene will make it possible to perpetuate these results by reducing viral transmission, the only unknown, the reopening procedure which can only be started after being surrounded by precautions aimed at ensuring the understanding of the population. CLINICALTRIAL Algeria, Covid-19, pandemic, hydroxychloroquin, azithromycin, case fatality rate

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