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Clustering analysis of countries using the COVID-19 cases dataset.

ABSTRACT: There is a worldwide effort of the research community to explore the medical, economic and sociologic impact of the COVID-19 pandemic. Many different disciplines try to find solutions and drive strategies to a great variety of different very crucial problems. The present study presents a novel analysis which results to clustering countries with respect to active cases, active cases per population and active cases per population and per area based on Johns Hopkins epidemiological data. The presented cluster results could be useful to a variety of different policy makers, such as physicians and managers of the health sector, economy/finance experts, politicians and even to sociologists. In addition, our work suggests a new specially designed clustering algorithm adapted to the request for comparison of the various COVID time-series of different countries.

SUBMITTER: Zarikas V

PROVIDER: S-EPMC7258836 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Clustering analysis of countries using the COVID-19 cases dataset.

Zarikas Vasilios V Poulopoulos Stavros G SG Gareiou Zoe Z Zervas Efthimios E

Data in brief 20200529

There is a worldwide effort of the research community to explore the medical, economic and sociologic impact of the COVID-19 pandemic. Many different disciplines try to find solutions and drive strategies to a great variety of different very crucial problems. The present study presents a novel analysis which results to clustering countries with respect to active cases, active cases per population and active cases per population and per area based on Johns Hopkins epidemiological data. The presen ...[more]

PMID: 32523977

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Project description:ObjectiveTo rank and score 180 countries according to COVID-19 cases and fatality in 2020 and compare the results to existing pandemic vulnerability prediction models and results generated by standard epidemiological scoring techniques.SettingOne hundred and eighty countries' patients with COVID-19 and fatality data representing the healthcare system preparedness and performance in combating the pandemic in 2020.DesignUsing the retrospective daily COVID-19 data in 2020 broken into 24 half-month periods, we applied unsupervised machine learning techniques, in particular, hierarchical clustering analysis to cluster countries into five groups within each period according to their cumulative COVID-19 fatality per day over the year and cumulative COVID-19 cases per million population per day over the half-month period. We used the average of the period scores to assign countries' final scores for each measure.Primary outcomeThe primary outcomes are the COVID-19 cases and fatality grades in 2020.ResultsThe United Arab Emirates and the USA with F in COVID-19 cases, achieved A or B in the fatality scores. Belgium and Sweden ranked F in both scores. Although no African country ranked F for COVID-19 cases, several African countries such as Gambia and Liberia had F for fatality scores. More developing countries ranked D and F in fatality than in COVID-19 case rankings. The classic epidemiological measures such as averages and rates have a relatively good correlation with our methodology, but past predictions failed to forecast the COVID-19 countries' preparedness.ConclusionCOVID-19 fatality can be a good proxy for countries' resources and system's resilience in managing the pandemic. These findings suggest that countries' economic and sociopolitical factors may behave in a more complex way as were believed. To explore these complex epidemiological associations, models can benefit enormously by taking advantage of methods developed in computer science and machine learning.

Project description:BackgroundRecurring COVID-19 waves highlight the need for tools able to quantify transmission risk, and identify geographical areas at risk of outbreaks. Local outbreak risk depends on complex immunity patterns resulting from previous infections, vaccination, waning and immune escape, alongside other factors (population density, social contact patterns). Immunity patterns are spatially and demographically heterogeneous, and are challenging to capture in country-level forecast models.MethodsWe used a spatiotemporal regression model to forecast subnational case and death counts and applied it to three EU countries as test cases: France, Czechia, and Italy. Cases in local regions arise from importations or local transmission. Our model produces age-stratified forecasts given age-stratified data, and links reported case counts to routinely collected covariates (e.g. test number, vaccine coverage). We assessed the predictive performance of our model up to four weeks ahead using proper scoring rules and compared it to the European COVID-19 Forecast Hub ensemble model. Using simulations, we evaluated the impact of variations in transmission on the forecasts. We developed an open-source RShiny App to visualise the forecasts and scenarios.ResultsAt a national level, the median relative difference between our median weekly case forecasts and the data up to four weeks ahead was 25% (IQR: 12-50%) over the prediction period. The accuracy decreased as the forecast horizon increased (on average 24% increase in the median ranked probability score per added week), while the accuracy of death forecasts was more stable. Beyond two weeks, the model generated a narrow range of likely transmission dynamics. The median national case forecasts showed similar accuracy to forecasts from the European COVID-19 Forecast Hub ensemble model, but the prediction interval was narrower in our model. Generating forecasts under alternative transmission scenarios was therefore key to capturing the range of possible short-term transmission dynamics.DiscussionOur model captures changes in local COVID-19 outbreak dynamics, and enables quantification of short-term transmission risk at a subnational level. The outputs of the model improve our ability to identify areas where outbreaks are most likely, and are available to a wide range of public health professionals through the Shiny App we developed.

Dataset Information

Clustering analysis of countries using the COVID-19 cases dataset.

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Clustering analysis of countries using the COVID-19 cases dataset.

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