hospitalization

2019 Novel Coronavirus COVID-19 (2019-nCoV) Visual Dashboard and Map:
https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

• Confirmed Cases by Country/Region/Sovereignty
• Confirmed Cases by Province/State/Dependency
• Deaths
• Recovered

Downloadable data:
https://github.com/CSSEGISandData/COVID-19

Additional Information about the Visual Dashboard:
https://systems.jhu.edu/research/public-health/ncov

Updated to May 13, 2021. World COVID-19 daily cases with basemap, starting from January 22, 2020.

The complete COVID-19 dataset is a collection of the COVID-19 data maintained by Our World in Data and is updated daily. This dataset includes data on confirmed cases, deaths, hospitalisations, and testing, as well as other variables of potential interest. A full description of each of the data columns can be found on the OWID Codebook

Unlock the Insights: Dive into the Comprehensive COVID-19 Dataset and Uncover Key Patterns, Trends, and Impacts Worldwide. Empower Your Analysis with Rich, Reliable, and Up-to-Date Data.

The COVID-19 dataset provides a comprehensive collection of information related to the global pandemic. It encompasses various aspects such as the number of cases, deaths, recoveries, testing, and more. The dataset serves as a valuable resource for researchers, analysts, and individuals seeking to understand the impact and spread of the virus.

The dataset is compiled from reputable sources, including official government reports, health organizations, and reliable data repositories. It ensures the accuracy and reliability of the information, making it a trusted source for COVID-19 data analysis.

The dataset is inspired by the need for reliable and up-to-date information about the COVID-19 pandemic. It aims to provide a comprehensive resource that enables researchers, analysts, and individuals to gain insights, track trends, and make data-driven decisions to combat the global health crisis.

By leveraging this dataset, users can gain a deeper understanding of the pandemic's progression, identify patterns, and contribute to the ongoing efforts in managing and mitigating the impact of COVID-19.

Updates

• Notice of data discontinuation: Since the start of the pandemic, AP has reported case and death counts from data provided by Johns Hopkins University. Johns Hopkins University has announced that they will stop their daily data collection efforts after March 10. As Johns Hopkins stops providing data, the AP will also stop collecting daily numbers for COVID cases and deaths. The HHS and CDC now collect and visualize key metrics for the pandemic. AP advises using those resources when reporting on the pandemic going forward.

  • CDC Weekly case and death counts (national and state level)
  • CDC County level cases and deaths
  • HHS New hospital admissions
  • CDC NowCast COVID variant proportions (national and regional level)

• April 9, 2020

  • The population estimate data for New York County, NY has been updated to include all five New York City counties (Kings County, Queens County, Bronx County, Richmond County and New York County). This has been done to match the Johns Hopkins COVID-19 data, which aggregates counts for the five New York City counties to New York County.

• April 20, 2020

  • Johns Hopkins death totals in the US now include confirmed and probable deaths in accordance with CDC guidelines as of April 14. One significant result of this change was an increase of more than 3,700 deaths in the New York City count. This change will likely result in increases for death counts elsewhere as well. The AP does not alter the Johns Hopkins source data, so probable deaths are included in this dataset as well.

• April 29, 2020

  • The AP is now providing timeseries data for counts of COVID-19 cases and deaths. The raw counts are provided here unaltered, along with a population column with Census ACS-5 estimates and calculated daily case and death rates per 100,000 people. Please read the updated caveats section for more information.

• September 1st, 2020

  • Johns Hopkins is now providing counts for the five New York City counties individually.

• February 12, 2021

  • The Ohio Department of Health recently announced that as many as 4,000 COVID-19 deaths may have been underreported through the state’s reporting system, and that the "daily reported death counts will be high for a two to three-day period."
  • Because deaths data will be anomalous for consecutive days, we have chosen to freeze Ohio's rolling average for daily deaths at the last valid measure until Johns Hopkins is able to back-distribute the data. The raw daily death counts, as reported by Johns Hopkins and including the backlogged death data, will still be present in the new_deaths column.

• February 16, 2021

  - Johns Hopkins has reconciled Ohio's historical deaths data with the state.

  Overview

The AP is using data collected by the Johns Hopkins University Center for Systems Science and Engineering as our source for outbreak caseloads and death counts for the United States and globally.

The Hopkins data is available at the county level in the United States. The AP has paired this data with population figures and county rural/urban designations, and has calculated caseload and death rates per 100,000 people. Be aware that caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.

This data is from the Hopkins dashboard that is updated regularly throughout the day. Like all organizations dealing with data, Hopkins is constantly refining and cleaning up their feed, so there may be brief moments where data does not appear correctly. At this link, you’ll find the Hopkins daily data reports, and a clean version of their feed.

The AP is updating this dataset hourly at 45 minutes past the hour.

To learn more about AP's data journalism capabilities for publishers, corporations and financial institutions, go here or email kromano@ap.org.

Queries

Use AP's queries to filter the data or to join to other datasets we've made available to help cover the coronavirus pandemic

• Filter cases by state here

• Rank states by their status as current hotspots. Calculates the 7-day rolling average of new cases per capita in each state: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=481e82a4-1b2f-41c2-9ea1-d91aa4b3b1ac

• Find recent hotspots within your state by running a query to calculate the 7-day rolling average of new cases by capita in each county: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=b566f1db-3231-40fe-8099-311909b7b687&showTemplatePreview=true

• Join county-level case data to an earlier dataset released by AP on local hospital capacity here. To find out more about the hospital capacity dataset, see the full details.

• Pull the 100 counties with the highest per-capita confirmed cases here

• Rank all the counties by the highest per-capita rate of new cases in the past 7 days here. Be aware that because this ranks per-capita caseloads, very small counties may rise to the very top, so take into account raw caseload figures as well.

Interactive

The AP has designed an interactive map to track COVID-19 cases reported by Johns Hopkins.

@(https://datawrapper.dwcdn.net/nRyaf/15/)

Interactive Embed Code

<iframe title="USA counties (2018) choropleth map Mapping COVID-19 cases by county" aria-describedby="" id="datawrapper-chart-nRyaf" src="https://datawrapper.dwcdn.net/nRyaf/10/" scrolling="no" frameborder="0" style="width: 0; min-width: 100% !important;" height="400"></iframe><script type="text/javascript">(function() {'use strict';window.addEventListener('message', function(event) {if (typeof event.data['datawrapper-height'] !== 'undefined') {for (var chartId in event.data['datawrapper-height']) {var iframe = document.getElementById('datawrapper-chart-' + chartId) || document.querySelector("iframe[src*='" + chartId + "']");if (!iframe) {continue;}iframe.style.height = event.data['datawrapper-height'][chartId] + 'px';}}});})();</script>

Caveats

• This data represents the number of cases and deaths reported by each state and has been collected by Johns Hopkins from a number of sources cited on their website.
• In some cases, deaths or cases of people who've crossed state lines -- either to receive treatment or because they became sick and couldn't return home while traveling -- are reported in a state they aren't currently in, because of state reporting rules.
• In some states, there are a number of cases not assigned to a specific county -- for those cases, the county name is "unassigned to a single county"
• This data should be credited to Johns Hopkins University's COVID-19 tracking project. The AP is simply making it available here for ease of use for reporters and members.
• Caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.
• Population estimates at the county level are drawn from 2014-18 5-year estimates from the American Community Survey.
• The Urban/Rural classification scheme is from the Center for Disease Control and Preventions's National Center for Health Statistics. It puts each county into one of six categories -- from Large Central Metro to Non-Core -- according to population and other characteristics. More details about the classifications can be found here.

Johns Hopkins timeseries data - Johns Hopkins pulls data regularly to update their dashboard. Once a day, around 8pm EDT, Johns Hopkins adds the counts for all areas they cover to the timeseries file. These counts are snapshots of the latest cumulative counts provided by the source on that day. This can lead to inconsistencies if a source updates their historical data for accuracy, either increasing or decreasing the latest cumulative count. - Johns Hopkins periodically edits their historical timeseries data for accuracy. They provide a file documenting all errors in their timeseries files that they have identified and fixed here

Attribution

This data should be credited to Johns Hopkins University COVID-19 tracking project

Abstract

JHU Coronavirus COVID-19 Global Cases, by country

Documentation

PHS is updating the Coronavirus Global Cases dataset weekly, Monday, Wednesday and Friday from Cloud Marketplace.

This data comes from the data repository for the 2019 Novel Coronavirus Visual Dashboard operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). This database was created in response to the Coronavirus public health emergency to track reported cases in real-time. The data include the location and number of confirmed COVID-19 cases, deaths, and recoveries for all affected countries, aggregated at the appropriate province or state. It was developed to enable researchers, public health authorities and the general public to track the outbreak as it unfolds. Additional information is available in the blog post.

Visual Dashboard (desktop): https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

Section 2

Included Data Sources are:

• World Health Organization (WHO): https://www.who.int/
• DXY.cn. Pneumonia. 2020. http://3g.dxy.cn/newh5/view/pneumonia.
• BNO News: https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/
• National Health Commission of the People’s Republic of China (NHC): http://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml
• China CDC (CCDC): http://weekly.chinacdc.cn/news/TrackingtheEpidemic.htm
• Hong Kong Department of Health: https://www.chp.gov.hk/en/features/102465.html
• Macau Government: https://www.ssm.gov.mo/portal/
• Taiwan CDC: https://sites.google.com/cdc.gov.tw/2019ncov/taiwan?authuser=0
• US CDC: https://www.cdc.gov/coronavirus/2019-ncov/index.html
• Government of Canada: https://www.canada.ca/en/public-health/services/diseases/coronavirus.html
• Australia Government Department of Health: https://www.health.gov.au/news/coronavirus-update-at-a-glance
• European Centre for Disease Prevention and Control (ECDC): https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases
• Ministry of Health Singapore (MOH): https://www.moh.gov.sg/covid-19
• Italy Ministry of Health: http://www.salute.gov.it/nuovocoronavirus
• 1Point3Arces: https://coronavirus.1point3acres.com/en
• WorldoMeters: https://www.worldometers.info/coronavirus/

%3C!-- --%3E

Section 3

**Terms of Use: **

This GitHub repo and its contents herein, including all data, mapping, and analysis, copyright 2020 Johns Hopkins University, all rights reserved, is provided to the public strictly for educational and academic research purposes. The Website relies upon publicly available data from multiple sources, that do not always agree. The Johns Hopkins University hereby disclaims any and all representations and warranties with respect to the Website, including accuracy, fitness for use, and merchantability. Reliance on the Website for medical guidance or use of the Website in commerce is strictly prohibited.

Section 4

**U.S. county-level characteristics relevant to COVID-19 **

Chin, Kahn, Krieger, Buckee, Balsari and Kiang (forthcoming) show that counties differ significantly in biological, demographic and socioeconomic factors that are associated with COVID-19 vulnerability. A range of publicly available county-specific data identifying these key factors, guided by international experiences and consideration of epidemiological parameters of importance, have been combined by the authors and are available for use:

https://github.com/mkiang/county_preparedness/

The World Health Organization reported 6932591 Coronavirus Deaths since the epidemic began. In addition, countries reported 766440796 Coronavirus Cases. This dataset provides - World Coronavirus Deaths- actual values, historical data, forecast, chart, statistics, economic calendar and news.

As of June 13, 2023, there have been almost 768 million cases of coronavirus (COVID-19) worldwide. The disease has impacted almost every country and territory in the world, with the United States confirming around 16 percent of all global cases.

COVID-19: An unprecedented crisis Health systems around the world were initially overwhelmed by the number of coronavirus cases, and even the richest and most prepared countries struggled. In the most vulnerable countries, millions of people lacked access to critical life-saving supplies, such as test kits, face masks, and respirators. However, several vaccines have been approved for use, and more than 13 billion vaccine doses had already been administered worldwide as of March 2023.

The coronavirus in the United Kingdom Over 202 thousand people have died from COVID-19 in the UK, which is the highest number in Europe. The tireless work of the National Health Service (NHS) has been applauded, but the country’s response to the crisis has drawn criticism. The UK was slow to start widespread testing, and the launch of a COVID-19 contact tracing app was delayed by months. However, the UK’s rapid vaccine rollout has been a success story, and around 53.7 million people had received at least one vaccine dose as of July 13, 2022.

The New York Times is releasing a series of data files with cumulative counts of coronavirus cases in the United States, at the state and county level, over time. We are compiling this time series data from state and local governments and health departments in an attempt to provide a complete record of the ongoing outbreak.

Since the first reported coronavirus case in Washington State on Jan. 21, 2020, The Times has tracked cases of coronavirus in real time as they were identified after testing. Because of the widespread shortage of testing, however, the data is necessarily limited in the picture it presents of the outbreak.

We have used this data to power our maps and reporting tracking the outbreak, and it is now being made available to the public in response to requests from researchers, scientists and government officials who would like access to the data to better understand the outbreak.

The data begins with the first reported coronavirus case in Washington State on Jan. 21, 2020. We will publish regular updates to the data in this repository.

As of May 2, 2023, the outbreak of the coronavirus disease (COVID-19) had been confirmed in almost every country in the world. The virus had infected over 687 million people worldwide, and the number of deaths had reached almost 6.87 million. The most severely affected countries include the U.S., India, and Brazil.

COVID-19: background information COVID-19 is a novel coronavirus that had not previously been identified in humans. The first case was detected in the Hubei province of China at the end of December 2019. The virus is highly transmissible and coughing and sneezing are the most common forms of transmission, which is similar to the outbreak of the SARS coronavirus that began in 2002 and was thought to have spread via cough and sneeze droplets expelled into the air by infected persons.

Naming the coronavirus disease Coronaviruses are a group of viruses that can be transmitted between animals and people, causing illnesses that may range from the common cold to more severe respiratory syndromes. In February 2020, the International Committee on Taxonomy of Viruses and the World Health Organization announced official names for both the virus and the disease it causes: SARS-CoV-2 and COVID-19, respectively. The name of the disease is derived from the words corona, virus, and disease, while the number 19 represents the year that it emerged.

Originally sourced from https://ourworldindata.org/coronavirus-source-data

Synced daily

Update 12/04/2020

The data sources have been updated to use JHU data:

From OWID:

​> On 30 November 2020, we changed our source for confirmed cases and deaths to the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University. Our previous source for confirmed cases and deaths, the European Centre for Disease Prevention and Control (ECDC), had announced in November 2020 that it would switch from a daily to a weekly reporting schedule from December. Our World in Data therefore had to transition away from the ECDC as a source to continue to provide daily updates of confirmed cases and deaths. The data last sourced from the ECDC remains available as an archive in the ecdc folder. The format (variable names and types) of our complete COVID-19 dataset remains the same.

Based on a comparison of coronavirus deaths in 210 countries relative to their population, Peru had the most losses to COVID-19 up until July 13, 2022. As of the same date, the virus had infected over 557.8 million people worldwide, and the number of deaths had totaled more than 6.3 million. Note, however, that COVID-19 test rates can vary per country. Additionally, big differences show up between countries when combining the number of deaths against confirmed COVID-19 cases. The source seemingly does not differentiate between "the Wuhan strain" (2019-nCOV) of COVID-19, "the Kent mutation" (B.1.1.7) that appeared in the UK in late 2020, the 2021 Delta variant (B.1.617.2) from India or the Omicron variant (B.1.1.529) from South Africa.

The difficulties of death figures

This table aims to provide a complete picture on the topic, but it very much relies on data that has become more difficult to compare. As the coronavirus pandemic developed across the world, countries already used different methods to count fatalities, and they sometimes changed them during the course of the pandemic. On April 16, for example, the Chinese city of Wuhan added a 50 percent increase in their death figures to account for community deaths. These deaths occurred outside of hospitals and went unaccounted for so far. The state of New York did something similar two days before, revising their figures with 3,700 new deaths as they started to include “assumed” coronavirus victims. The United Kingdom started counting deaths in care homes and private households on April 29, adjusting their number with about 5,000 new deaths (which were corrected lowered again by the same amount on August 18). This makes an already difficult comparison even more difficult. Belgium, for example, counts suspected coronavirus deaths in their figures, whereas other countries have not done that (yet). This means two things. First, it could have a big impact on both current as well as future figures. On April 16 already, UK health experts stated that if their numbers were corrected for community deaths like in Wuhan, the UK number would change from 205 to “above 300”. This is exactly what happened two weeks later. Second, it is difficult to pinpoint exactly which countries already have “revised” numbers (like Belgium, Wuhan or New York) and which ones do not. One work-around could be to look at (freely accessible) timelines that track the reported daily increase of deaths in certain countries. Several of these are available on our platform, such as for Belgium, Italy and Sweden. A sudden large increase might be an indicator that the domestic sources changed their methodology.

Where are these numbers coming from?

The numbers shown here were collected by Johns Hopkins University, a source that manually checks the data with domestic health authorities. For the majority of countries, this is from national authorities. In some cases, like China, the United States, Canada or Australia, city reports or other various state authorities were consulted. In this statistic, these separately reported numbers were put together. For more information or other freely accessible content, please visit our dedicated Facts and Figures page.

On March 10, 2023, the Johns Hopkins Coronavirus Resource Center ceased its collecting and reporting of global COVID-19 data. For updated cases, deaths, and vaccine data please visit: World Health Organization (WHO)For more information, visit the Johns Hopkins Coronavirus Resource Center.COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.DOI: https://doi.org/10.6084/m9.figshare.125529863/7/2022 - Adjusted the rate of active cases calculation in the U.S. to reflect the rates of serious and severe cases due nearly completely dominant Omicron variant.6/24/2020 - Expanded Case Rates discussion to include fix on 6/23 for calculating active cases.6/22/2020 - Added Executive Summary and Subsequent Outbreaks sectionsRevisions on 6/10/2020 based on updated CDC reporting. This affects the estimate of active cases by revising the average duration of cases with hospital stays downward from 30 days to 25 days. The result shifted 76 U.S. counties out of Epidemic to Spreading trend and no change for national level trends.Methodology update on 6/2/2020: This sets the length of the tail of new cases to 6 to a maximum of 14 days, rather than 21 days as determined by the last 1/3 of cases. This was done to align trends and criteria for them with U.S. CDC guidance. The impact is areas transition into Controlled trend sooner for not bearing the burden of new case 15-21 days earlier.Correction on 6/1/2020Discussion of our assertion of an abundance of caution in assigning trends in rural counties added 5/7/2020. Revisions added on 4/30/2020 are highlighted.Revisions added on 4/23/2020 are highlighted.Executive SummaryCOVID-19 Trends is a methodology for characterizing the current trend for places during the COVID-19 global pandemic. Each day we assign one of five trends: Emergent, Spreading, Epidemic, Controlled, or End Stage to geographic areas to geographic areas based on the number of new cases, the number of active cases, the total population, and an algorithm (described below) that contextualize the most recent fourteen days with the overall COVID-19 case history. Currently we analyze the countries of the world and the U.S. Counties. The purpose is to give policymakers, citizens, and analysts a fact-based data driven sense for the direction each place is currently going. When a place has the initial cases, they are assigned Emergent, and if that place controls the rate of new cases, they can move directly to Controlled, and even to End Stage in a short time. However, if the reporting or measures to curtail spread are not adequate and significant numbers of new cases continue, they are assigned to Spreading, and in cases where the spread is clearly uncontrolled, Epidemic trend.We analyze the data reported by Johns Hopkins University to produce the trends, and we report the rates of cases, spikes of new cases, the number of days since the last reported case, and number of deaths. We also make adjustments to the assignments based on population so rural areas are not assigned trends based solely on case rates, which can be quite high relative to local populations.Two key factors are not consistently known or available and should be taken into consideration with the assigned trend. First is the amount of resources, e.g., hospital beds, physicians, etc.that are currently available in each area. Second is the number of recoveries, which are often not tested or reported. On the latter, we provide a probable number of active cases based on CDC guidance for the typical duration of mild to severe cases.Reasons for undertaking this work in March of 2020:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-25 days + 5% from past 26-49 days - total deaths. On 3/17/2022, the U.S. calculation was adjusted to: Active Cases = 100% of new cases in past 14 days + 6% from past 15-25 days + 3% from past 26-49 days - total deaths. Sources: https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e4.htm https://covid.cdc.gov/covid-data-tracker/#variant-proportions If a new variant arrives and appears to cause higher rates of serious cases, we will roll back this adjustment. We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source

The table covid19_jhu_csse_summary is part of the dataset Coronavirus COVID-19 Global Cases, available at https://stanford.redivis.com/datasets/rxta-4v35cgyzf. It contains 390476 rows across 13 variables.

COVID-19, caused by the novel coronavirus SARS-CoV-2, emerged in late 2019 and rapidly spread across the globe, leading to an unprecedented pandemic. The virus has significantly impacted public health, economies, and daily life worldwide. Monitoring and understanding the spread and impact of COVID-19 is crucial for mitigating its effects and planning effective responses.

This dataset aims to provide comprehensive data on COVID-19 cases, deaths, and recoveries across 230 countries.

Clinical data from patients hospitalised with COVID19 globally shared as a part of the ISARIC Clinical Characterisation Group collaboration.

In collaboration with The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), The Infectious Diseases Data Observatory (IDDO) has assembled the world’s largest global database on COVID-19 clinical data with detailed individual patient data on 657,312 hospitalised individuals from 1,297 institutions across 45 countries.

The full dataset is available to all institutions contributing data via ncov@isaric.org. Individuals and institutions who have not contributed data to the dataset may apply for access via https://www.iddo.org/covid19/data-sharing/accessing-data under the following license https://www.iddo.org/document/covid-19-data-transfer-agreement

Context

From World Health Organization - On 31 December 2019, WHO was alerted to several cases of pneumonia in Wuhan City, Hubei Province of China. The virus did not match any other known virus. This raised concern because when a virus is new, we do not know how it affects people.

So daily level information on the affected people can give some interesting insights when it is made available to the broader data science community.

Johns Hopkins University has made an excellent dashboard using the affected cases data. Data is extracted from the google sheets associated and made available here.

Edited

Now data is available as csv files in the Johns Hopkins Github repository. Please refer to the github repository for the Terms of Use details. Uploading it here for using it in Kaggle kernels and getting insights from the broader DS community.

Content 2019 Novel Coronavirus (2019-nCoV) is a virus (more specifically, a coronavirus) identified as the cause of an outbreak of respiratory illness first detected in Wuhan, China. Early on, many of the patients in the outbreak in Wuhan, China reportedly had some link to a large seafood and animal market, suggesting animal-to-person spread. However, a growing number of patients reportedly have not had exposure to animal markets, indicating person-to-person spread is occurring. At this time, it’s unclear how easily or sustainably this virus is spreading between people - CDC

This dataset has daily level information on the number of affected cases, deaths and recovery from 2019 novel coronavirus. Please note that this is a time series data and so the number of cases on any given day is the cumulative number.

The data is available from 22 Jan, 2020 to 30 Dec, 2020.

Sources

JHU confirmed covid datasets.

A COVID-19 dataset that is updated daily and includes data on confirmed cases, deaths, excess mortality, policies, hospitalizations (and intensive care unit admissions), testing, and vaccinations as well as other variables of potential interest. Data is collected, aggregated, compiled, and documented by the Our World in Data team using different data sources repositories such as from John Hopkins University Center for Systems Science and Engineering (CSSE), European Centre for Disease Prevention and Control (ECDC), WHO, and country official data.

COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.Revisions added on 4/23/2020 are highlighted.Revisions added on 4/30/2020 are highlighted.Discussion of our assertion of an abundance of caution in assigning trends in rural counties added 5/7/2020. Correction on 6/1/2020Methodology update on 6/2/2020: This sets the length of the tail of new cases to 6 to a maximum of 14 days, rather than 21 days as determined by the last 1/3 of cases. This was done to align trends and criteria for them with U.S. CDC guidance. The impact is areas transition into Controlled trend sooner for not bearing the burden of new case 15-21 days earlier.Reasons for undertaking this work:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-30 days + 5% from past 31-56 days - total deaths.We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source used as basis:Stephen A. Lauer, MS, PhD *; Kyra H. Grantz, BA *; Qifang Bi, MHS; Forrest K. Jones, MPH; Qulu Zheng, MHS; Hannah R. Meredith, PhD; Andrew S. Azman, PhD; Nicholas G. Reich, PhD; Justin Lessler, PhD. 2020. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Annals of Internal Medicine DOI: 10.7326/M20-0504.New Cases per Day (NCD) = Measures the daily spread of COVID-19. This is the basis for all rates. Back-casting revisions: In the Johns Hopkins’ data, the structure is to provide the cumulative number of cases per day, which presumes an ever-increasing sequence of numbers, e.g., 0,0,1,1,2,5,7,7,7, etc. However, revisions do occur and would look like, 0,0,1,1,2,5,7,7,6. To accommodate this, we revised the lists to eliminate decreases, which make this list look like, 0,0,1,1,2,5,6,6,6.Reporting Interval: In the early weeks, Johns Hopkins' data provided reporting every day regardless of change. In late April, this changed allowing for days to be skipped if no new data was available. The day was still included, but the value of total cases was set to Null. The processing therefore was updated to include tracking of the spacing between intervals with valid values.100 News Cases in a day as a spike threshold: Empirically, this is based on COVID-19’s rate of spread, or r0 of ~2.5, which indicates each case will infect between two and three other people. There is a point at which each administrative area’s capacity will not have the resources to trace and account for all contacts of each patient. Thus, this is an indicator of uncontrolled or epidemic trend. Spiking activity in combination with the rate of new cases is the basis for determining whether an area has a spreading or epidemic trend (see below). Source used as basis:World Health Organization (WHO). 16-24 Feb 2020. Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19). Obtained online.Mean of Recent Tail of NCD = Empirical, and a COVID-19-specific basis for establishing a recent trend. The recent mean of NCD is taken from the most recent fourteen days. A minimum of 21 days of cases is required for analysis but cannot be considered reliable. Thus, a preference of 42 days of cases ensures much higher reliability. This analysis is not explanatory and thus, merely represents a likely trend. The tail is analyzed for the following:Most recent 2 days: In terms of likelihood, this does not mean much, but can indicate a reason for hope and a basis to share positive change that is not yet a trend. There are two worthwhile indicators:Last 2 days count of new cases is less than any in either the past five or 14 days. Past 2 days has only one or fewer new cases – this is an extremely positive outcome if the rate of testing has continued at the same rate as the previous 5 days or 14 days. Most recent 5 days: In terms of likelihood, this is more meaningful, as it does represent at short-term trend. There are five worthwhile indicators:Past five days is greater than past 2 days and past 14 days indicates the potential of the past 2 days being an aberration. Past five days is greater than past 14 days and less than past 2 days indicates slight positive trend, but likely still within peak trend time frame.Past five days is less than the past 14 days. This means a downward trend. This would be an