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 late January, 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.

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

A. SUMMARY Medical provider confirmed COVID-19 cases and confirmed COVID-19 related deaths in San Francisco, CA aggregated by several different geographic areas and normalized by 2016-2020 American Community Survey (ACS) 5-year estimates for population data to calculate rate per 10,000 residents.

On September 12, 2021, a new case definition of COVID-19 was introduced that includes criteria for enumerating new infections after previous probable or confirmed infections (also known as reinfections). A reinfection is defined as a confirmed positive PCR lab test more than 90 days after a positive PCR or antigen test. The first reinfection case was identified on December 7, 2021.

Cases and deaths are both mapped to the residence of the individual, not to where they were infected or died. For example, if one was infected in San Francisco at work but lives in the East Bay, those are not counted as SF Cases or if one dies in Zuckerberg San Francisco General but is from another county, that is also not counted in this dataset.

Dataset is cumulative and covers cases going back to 3/2/2020 when testing began.

Geographic areas summarized are: 1. Analysis Neighborhoods 2. Census Tracts 3. Census Zip Code Tabulation Areas

B. HOW THE DATASET IS CREATED Addresses from medical data are geocoded by the San Francisco Department of Public Health (SFDPH). Those addresses are spatially joined to the geographic areas. Counts are generated based on the number of address points that match each geographic area. The 2016-2020 American Community Survey (ACS) population estimates provided by the Census are used to create a rate which is equal to ([count] / [acs_population]) * 10000) representing the number of cases per 10,000 residents.

C. UPDATE PROCESS Geographic analysis is scripted by SFDPH staff and synced to this dataset daily at 7:30 Pacific Time.

D. HOW TO USE THIS DATASET San Francisco population estimates for geographic regions can be found in a view based on the San Francisco Population and Demographic Census dataset. These population estimates are from the 2016-2020 5-year American Community Survey (ACS).

Privacy rules in effect To protect privacy, certain rules are in effect: 1. Case counts greater than 0 and less than 10 are dropped - these will be null (blank) values 2. Death counts greater than 0 and less than 10 are dropped - these will be null (blank) values 3. Cases and deaths dropped altogether for areas where acs_population < 1000

Rate suppression in effect where counts lower than 20 Rates are not calculated unless the case count is greater than or equal to 20. Rates are generally unstable at small numbers, so we avoid calculating them directly. We advise you to apply the same approach as this is best practice in epidemiology.

A note on Census ZIP Code Tabulation Areas (ZCTAs) ZIP Code Tabulation Areas are special boundaries created by the U.S. Census based on ZIP Codes developed by the USPS. They are not, however, the same thing. ZCTAs are areal representations of routes. Read how the Census develops ZCTAs on their website.

Row included for Citywide case counts, incidence rate, and deaths A single row is included that has the Citywide case counts and incidence rate. This can be used for comparisons. Citywide will capture all cases regardless of address quality. While some cases cannot be mapped to sub-areas like Census Tracts, ongoing data quality efforts result in improved mapping on a rolling basis.

E. CHANGE LOG

• 9/11/2023 - data on COVID-19 cases and deaths summarized by geography are no longer being updated. This data is currently through 9/6/2023 and will not include any new data after this date.
• 4/6/2023 - the State implemented system updates to improve the integrity of historical data.
• 2/21/2023 - system updates to improve reliability and accuracy of cases data were implemented.
• 1/31/2023 - updated “acs_population” column to reflect the 2020 Census Bureau American Community Survey (ACS) San Francisco Population estimates.
• 1/31/2023 - implemented system updates to streamline and improve our geo-coded data, resulting in small shifts in our case and death data by geography.
• 1/31/2023 - renamed column “last_updated_at” to “data_as_of”.
• 2/23/2022 - the New Cases Map dashboard began pulling from this dataset. To access Cases by Geography Over Time, please refer to this dataset.
• 1/22/2022 - system updates to improve timeliness and accuracy of cases and deaths data were implemented.
• 7/15/2022 - reinfections added to cases dataset. See section SUMMARY for more information on how reinfections are identified.
• 4/16/2021 - dataset updated to refresh with a five-day data lag.

Note: This dataset is no longer being updated as of June 2, 2025.

This dataset contains numbers of COVID-19 outbreaks and associated cases, categorized by setting, reported to CDPH since January 1, 2021.

AB 685 (Chapter 84, Statutes of 2020) and the Cal/OSHA COVID-19 Emergency Temporary Standards (Title 8, Subchapter 7, Sections 3205-3205.4) required non-healthcare employers in California to report workplace COVID-19 outbreaks to their local health department (LHD) between January 1, 2021 – December 31, 2022. Beginning January 1, 2023, non-healthcare employer reporting of COVID-19 outbreaks to local health departments is voluntary, unless a local order is in place. More recent data collected without mandated reporting may therefore be less representative of all outbreaks that have occurred, compared to earlier data collected during mandated reporting. Licensed health facilities continue to be mandated to report outbreaks to LHDs.

LHDs report confirmed outbreaks to the California Department of Public Health (CDPH) via the California Reportable Disease Information Exchange (CalREDIE), the California Connected (CalCONNECT) system, or other established processes. Data are compiled and categorized by setting by CDPH. Settings are categorized by U.S. Census industry codes. Total outbreaks and cases are included for individual industries as well as for broader industrial sectors.

The first dataset includes numbers of outbreaks in each setting by month of onset, for outbreaks reported to CDPH since January 1, 2021. This dataset includes some outbreaks with onset prior to January 1 that were reported to CDPH after January 1; these outbreaks are denoted with month of onset “Before Jan 2021.” The second dataset includes cumulative numbers of COVID-19 outbreaks with onset after January 1, 2021, categorized by setting. Due to reporting delays, the reported numbers may not reflect all outbreaks that have occurred as of the reporting date; additional outbreaks may have occurred that have not yet been reported to CDPH.

While many of these settings are workplaces, cases may have occurred among workers, other community members who visited the setting, or both. Accordingly, these data do not distinguish between outbreaks involving only workers, outbreaks involving only residents or patrons, or outbreaks involving both.

Several additional data limitations should be kept in mind:

• Outbreaks are classified as “Insufficient information” for outbreaks where not enough information was available for CDPH to assign an industry code.

• Some sectors, particularly congregate residential settings, may have increased testing and therefore increased likelihood of outbreak recognition and reporting. As a result, in congregate residential settings, the number of outbreak-associated cases may be more accurate.

• However, in most settings, outbreak and case counts are likely underestimates. For most cases, it is not possible to identify the source of exposure, as many cases have multiple possible exposures.

• Because some settings have been at times been closed or open with capacity restrictions, numbers of outbreak reports in those settings do not reflect COVID-19 transmission risk.

• The number of outbreaks in different settings will depend on the number of different workplaces in each setting. More outbreaks would be expected in settings with many workplaces compared to settings with few workplaces.

This dataset contains counts of COVID-19 cases and deaths in North Carolina from March 2, 2020 to May 31, 2021. The data was extracted from NC Department of Health and Human Services' NC COVID-19 dashboard: Daily Cases and Deaths Metrics. This dataset is an archive - it is not being updated. Data Source: NCDHHS (2021). Daily Cases and Deaths Metrics (Version 1.3) [Data set]. https://covid19.ncdhhs.gov/dashboard/data-behind-dashboards

Context

As we enter into the latter half of the second year of the Coronavirus pandemic, transmission has become the keyword as more variants emerge. In this dataset, I thought to shed some light on the relationship between transmission types and death rates. This dataset contains the number of cases by region in Canada in 2021 by their respective transmission methods and death rates. I also added the perceived health by region in Canada in 2020 as compared to 2019.

Content

The dataset consists of two csv files: transmission & death.csv and Perceived Health.csv.

transmission & death.csv: Case counts by region in Canada categorized by transmission methods and death status. This data is provided by the Public Health Agency of Canada. The original data set contains age and gender details, which I combined columns into one to focus on the transmission vs. death investigation. This file contains case counts from January 15, 2020 to September 5, 2021.

Perceived Health.csv is the perceived health by region in Canada based on the Canadian Community Health Survey released on September 8, 2021.

Column Description

transmission & death dataset transmission & death.csv:

Geography: For the purpose of this study, geography is the Canadian regions of Atlantic, Quebec, Ontario and Nunavut, Prairies and Northwest Territories, and British Columbia and Yukon

Transmission: For the purpose of this study, transmission types are community exposures, travel exposures and not stated

Death statuses: For this study, death statuses are deceased, not deceased and not stated

Perceived Health dataset Perceived Health.csv:

Geography: In this file, geography is broken down into Newfoundland and Labrador, Prince Edward Island, Nova Scotia, New Brunswick, Quebec, Ontario, Manitoba, Saskatchewan, Albert, and British Columbia

Indicators: Perceived health is broken down into very good or excellent and fair or poor

Age groups are broken down into 12 to 17 years, 18 to 34 years, 35 to 49 years, 50 to 64 years, and 65 years and over

Acknowledgements

Data provided for public use by Statistics Canada.

Inspiration

This dataset is meant to gain insight into the severity of symptoms of the coronavirus, as it relates to the type of transmission or the perceived health of the region in question.

Vaccinations in London Between 8 December 2020 and 15 September 2021 5,838,305 1st doses and 5,232,885 2nd doses have been administered to London residents.

Differences in vaccine roll out between London and the Rest of England London Rest of England Priority Group Vaccinations given Percentage vaccinated Vaccinations given Percentage vaccinated Group 1 Older Adult Care Home Residents 21,883 95% 275,964 96% Older Adult Care Home Staff 29,405 85% 381,637 88% Group 2 80+ years 251,021 83% 2,368,284 93% Health Care Worker 174,944 99% 1,139,243 100%* Group 3 75 - 79 years 177,665 90% 1,796,408 99% Group 4 70 - 74 years 252,609 90% 2,454,381 97% Clinically Extremely Vulnerable 278,967 88% 1,850,485 95% Group 5 65 - 69 years 285,768 90% 2,381,250 97% Group 6 At Risk or Carer (Under 65) 983,379 78% 6,093,082 88% Younger Adult Care Home Residents 3,822 92% 30,321 93% Group 7 60 - 64 years 373,327 92% 2,748,412 98% Group 8 55 - 59 years 465,276 91% 3,152,412 97% Group 9 50 - 54 years 510,132 90% 3,141,219 95% Data as at 15 September 2021 for age based groups and as at 12 September 2021 for non-age based groups * The number who have received their first dose exceeds the latest official estimate of the population for this group There is considerable uncertainty in the population denominators used to calculate the percentage vaccinated. Comparing implied vaccination rates for multiple sources of denominators provides some indication of uncertainty in the true values. Confidence is higher where the results from multiple sources agree more closely. Because the denominator sources are not fully independent of one another, users should interpret the range of values across sources as indicating the minimum range of uncertainty in the true value. The following datasets can be used to estimate vaccine uptake by age group for London:

ONS 2020 mid-year estimates (MYE). This is the population estimate used for age groups throughout the rest of the analysis.


Number of people ages 18 and over on the National Immunisation Management Service (NIMS)


ONS Public Health Data Asset (PHDA) dataset. This is a linked dataset combining the 2011 Census, the General Practice Extraction Service (GPES) data for pandemic planning and research and the Hospital Episode Statistics (HES). This data covers a subset of the population.

Vaccine roll out in London by Ethnic Group Understanding how vaccine uptake varies across different ethnic groups in London is complicated by two issues:

Ethnicity information for recipients is unavailable for a very large number of the vaccinations that have been delivered. As a result, estimates of vaccine uptake by ethnic group are highly sensitive to the assumptions about and treatment of the Unknown group in calculations of rates.

For vaccinations given to people aged 50 and over in London nearly 10% do not have ethnicity information available,

The accuracy of available population denominators by ethnic group is limited. Because ethnicity information is not captured in official estimates of births, deaths, and migration, the available population denominators typically rely on projecting forward patterns captured in the 2011 Census. Subsequent changes to these patterns, particularly with respect to international migration, leads to increasing uncertainty in the accuracy of denominators sources as we move further away from 2011.

Comparing estimated population sizes and implied vaccination rates for multiple sources of denominators provides some indication of uncertainty in the true values. Confidence is higher where the results from multiple sources agree more closely. Because the denominator sources are not fully independent of one another, users should interpret the range of values across sources as indicating the minimum range of uncertainty in the true value. The following population estimates are available by Ethnic group for London:

GLA Ethnic group population projections - 2016 as at 2021


ONS Population Denominators produced for Race Disparity Audit as at 2018


ETHPOP population projections produced by the University of Leeds as at 2020

Antibody prevalence estimates As part of the ONS Coronavirus (COVID-19) Infection Survey ONS publish a modelled estimate of the percent of the adult population testing positive for antibodies to Coronavirus by region. Antibodies can be generated by vaccination or previous infection.

Vaccine effects on cases, hospitalisations and deaths When the vaccine roll out began in December 2020 coronavirus cases, hospital admissions and deaths were rising steeply. The peak of infections came in London in early January 2021, before reducing during the national lockdown and as the vaccine roll out progressed. As the vaccine roll out began in older age groups the effect of vaccinations can be separated from the effect of national lockdown by comparing changes in cases, admissions and deaths

This file contains weekly data on confirmed COVID-19 cases and numbers of students thought to be self isolating at Higher Education Providers (HEPs) from the week to 04 November 2020 to the week to 07 April 2021. It also contains estimated weekly case rates from the week to 04 November 2020 to the week to 16 December 2020.

Dataset Description: Infected and Death Cases of Covid-19 in Bangladesh This dataset contains detailed information on Covid-19 cases in Bangladesh, focusing on the number of new cases and deaths reported. The data spans from September 27, 2020, to November 19, 2021. The dataset is structured with three primary columns:

Date: The date when the data was recorded, formatted as YYYY-MM-DD. New Cases: The number of new Covid-19 cases reported on the corresponding date. Deaths: The number of deaths attributed to Covid-19 on the corresponding date. Key Features: Time Range: Covers over a year of data, capturing various waves of the pandemic. Granularity: Daily records, providing detailed insights into the daily progression of the pandemic. Size: The dataset is compact, with a file size of 7.91 KB, making it easy to handle and analyze. Cite this paper

@InProceedings{10.1007/978-981-19-2445-3_38, author="Rahman, Ashifur and Hossain, Md. Akbar and Moon, Mohasina Jannat", editor="Hossain, Sazzad and Hossain, Md. Shahadat and Kaiser, M. Shamim and Majumder, Satya Prasad and Ray, Kanad", title="An LSTM-Based Forecast Of COVID-19 For Bangladesh", booktitle="Proceedings of International Conference on Fourth Industrial Revolution and Beyond 2021 ", year="2022", publisher="Springer Nature Singapore", address="Singapore", pages="551--561", abstract="Preoperative events can be predicted using deep learning-based forecasting techniques. It can help to improve future decision-making. Deep learning has traditionally been used to identify and evaluate adverse risks in a variety of major applications. Numerous prediction approaches are commonly applied to deal with forecasting challenges. The number of infected people, as well as the mortality rate of COVID-19, is increasing every day. Many countries, including India, Brazil, and the United States, were severely affected; however, since the very first case was identified, the transmission rate has decreased dramatically after a set time period. Bangladesh, on the other hand, was unable to keep the rate of infection low. In this situation, several methods have been developed to forecast the number of affected, time to recover, and the number of deaths. This research illustrates the ability of DL models to forecast the number of affected and dead people as a result of COVID-19, which is now regarded as a possible threat to humanity. As part of this study, we developed an LSTM based method to predict the next 100 days of death and newly identified COVID-19 cases in Bangladesh. To do this experiment we collect data on death and newly detected COVID-19 cases through Bangladesh's national COVID-19 help desk website. After collecting data we processed it to make a dataset for training our LSTM model. After completing the training, we predict our model with the test dataset. The result of our model is very robust on the basis of the training and testing dataset. Finally, we forecast the subsequent 100 days of deaths and newly infected COVID-19 cases in Bangladesh.", isbn="978-981-19-2445-3" }

Context

• Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus SARS-CoV2.
• Person to person transmission occurs via several different modes, mainly when people are in close proximity to one another through respiratory droplets.
• Mitigations by various countries have been put into place to limit the spread of this virus.

Content

• ConfirmedCasesByDateReported.csv
• ConfirmedCasesBySpecimenDate.csv
• Deaths.csv
• PatientNewAdmissions.csv
• PatientsInHospital.csv
• PatientsMVBeds.csv
• PCRTesting.csv
• Vaccinations.csv
• VaccinationsDaily.csv

Acknowledgements and Collection Methodology

Data downloaded from https://coronavirus.data.gov.uk

Version

• Version 11 - 25 - Various Files Updated.
• Version 10 - Added VaccinationsDaily File, data upto and including the 20th Jan 2021.
• Version 9 - Updated Deaths file, data upto and including the 20th Jan 2021.
• Version 8 - Updated ConfirmedCasesByDateReported and ConfirmedCasesBySpecimenDate files, data upto and including the 17th to 19th Jan 2021 respectively.
• Version 7 - Updated PatientNewAdmissions, PatientsInHospital and PatientsMVBeds files, data upto and including the 12th to 15th Jan 2020 depending on file.
• Version 6 - Updated PCR Testing file, data upto and including the 14th Jan 2021.
• Version 4 - Updated Vaccinations file, data upto and including the 3rd Jan 2021.
• Version 3 - Updated to include data unto and including the 28th December 2020. Additionally added data on the progress of Vaccinations.
• Version 2 - Updated to include data unto and including the 3rd November 2020.

ObjectiveTo create a data-driven definition of post-COVID conditions (PCC) by directly measure changes in symptomatology before and after a first COVID episode.Materials and methodsRetrospective cohort study using Optum® de-identified Electronic Health Record (EHR) dataset from the United States of persons of any age April 2020-September 2021. For each person with COVID (ICD-10-CM U07.1 “COVID-19” or positive test result), we selected up to 3 comparators. The final COVID symptom score was computed as the sum of new diagnoses weighted by each diagnosis’ ratio of incidence in COVID group relative to comparator group. For the subset of COVID cases diagnosed in September 2021, we compared the incidence of PCC using our data-driven definition with ICD-10-CM code U09.9 “Post-COVID Conditions”, first available in the US October 2021.ResultsThe final cohort contained 588,611 people with COVID, with mean age of 48 years and 38% male. Our definition identified 20% of persons developed PCC in follow-up. PCC incidence increased with age: (7.8% of persons aged 0–17, 17.3% aged 18–64, and 33.3% aged 65+) and did not change over time (20.0% among persons diagnosed with COVID in 2020 versus 20.3% in 2021). For cases diagnosed in September 2021, our definition identified 19.0% with PCC in follow-up as compared to 2.9% with U09.9 code in follow-up.ConclusionSymptom and U09.9 code-based definitions alone captured different populations. Maximal capture may consider a combined approach, particularly before the availability and routine utilization of specific ICD-10 codes and with the lack consensus-based definitions on the syndrome.

Odds ratios of COVID-19 infection from 1 July 2020 to 22 February 2021 among individuals living in under-65 households.

Changelog:

Update September 20, 2021: Data and overview updated to reflect data used in the September 15 story Over Half of States Have Rolled Back Public Health Powers in Pandemic. It includes 303 state or local public health leaders who resigned, retired or were fired between April 1, 2020 and Sept. 12, 2021. Previous versions of this dataset reflected data used in the Dec. 2020 and April 2021 stories.

Overview

Across the U.S., state and local public health officials have found themselves at the center of a political storm as they combat the worst pandemic in a century. Amid a fractured federal response, the usually invisible army of workers charged with preventing the spread of infectious disease has become a public punching bag.

In the midst of the coronavirus pandemic, at least 303 state or local public health leaders in 41 states have resigned, retired or been fired since April 1, 2020, according to an ongoing investigation by The Associated Press and KHN.

According to experts, that is the largest exodus of public health leaders in American history.

Many left due to political blowback or pandemic pressure, as they became the target of groups that have coalesced around a common goal — fighting and even threatening officials over mask orders and well-established public health activities like quarantines and contact tracing. Some left to take higher profile positions, or due to health concerns. Others were fired for poor performance. Dozens retired. An untold number of lower level staffers have also left.

The result is a further erosion of the nation’s already fragile public health infrastructure, which KHN and the AP documented beginning in 2020 in the Underfunded and Under Threat project.

Findings

The AP and KHN found that:

• One in five Americans live in a community that has lost its local public health department leader during the pandemic
• Top public health officials in 28 states have left state-level departments ## Using this data To filter for data specific to your state, use this query

To get total numbers of exits by state, broken down by state and local departments, use this query

Methodology

KHN and AP counted how many state and local public health leaders have left their jobs between April 1, 2020 and Sept. 12, 2021.

The government tasks public health workers with improving the health of the general population, through their work to encourage healthy living and prevent infectious disease. To that end, public health officials do everything from inspecting water and food safety to testing the nation’s babies for metabolic diseases and contact tracing cases of syphilis.

Many parts of the country have a health officer and a health director/administrator by statute. The analysis counted both of those positions if they existed. For state-level departments, the count tracks people in the top and second-highest-ranking job.

The analysis includes exits of top department officials regardless of reason, because no matter the reason, each left a vacancy at the top of a health agency during the pandemic. Reasons for departures include political pressure, health concerns and poor performance. Others left to take higher profile positions or to retire. Some departments had multiple top officials exit over the course of the pandemic; each is included in the analysis.

Reporters compiled the exit list by reaching out to public health associations and experts in every state and interviewing hundreds of public health employees. They also received information from the National Association of City and County Health Officials, and combed news reports and records.

Public health departments can be found at multiple levels of government. Each state has a department that handles these tasks, but most states also have local departments that either operate under local or state control. The population served by each local health department is calculated using the U.S. Census Bureau 2019 Population Estimates based on each department’s jurisdiction.

KHN and the AP have worked since the spring on a series of stories documenting the funding, staffing and problems around public health. A previous data distribution detailed a decade's worth of cuts to state and local spending and staffing on public health. That data can be found here.

Attribution

Findings and the data should be cited as: "According to a KHN and Associated Press report."

Is Data Missing?

If you know of a public health official in your state or area who has left that position between April 1, 2020 and Sept. 12, 2021 and isn't currently in our dataset, please contact authors Anna Maria Barry-Jester annab@kff.org, Hannah Recht hrecht@kff.org, Michelle Smith mrsmith@ap.org and Lauren Weber laurenw@kff.org.

This dataset include two .csv files containing the integrated dataset used by the COVID-19 School Dashboard website to report and maps confirmed school-related cases of COVID-19 in publicly funded elementary and secondary schools in Ontario, Canada, and connects this to data on school social background characteristics. One csv file reports cases from 2020-09-10 to 2021-04-14 (2020 school year) while the other csv file reports cases from 2021-09-13 to 2021-12-22 (2021 school year). Two accompanying .doc files are included to describe the variables in the .csv files.

This data has been restarted and published 8/25, going forward on Fridays. We are working on the metadata currently to better reflect this. All data is from 8/1 going forward, and now includes colleges.

As of July 1, 2021, the reporting of COVID-19 outbreaks within selected settings by facility name, number of cases, and deaths is no longer required by law, and this dataset will not be updated after June 30, 2021.
This dataset includes data reported to VDH on outbreaks that occurred in medical care facilities, residential or day programs licensed by Virginia Department of Health (VDH), Department of Social Services (DSS), or Department of Behavioral Health and Developmental Services (DBHDS), summer camps, and kindergarten (K)-12th grade schools in Virginia. The data included are the name of the facility, locality of the facility, date VDH is notified about the outbreak, status of the outbreak, and the number of associated cases and deaths. This data set was first published on December 18, 2020. This data set was last updated on June 25, 2021.

COVID-Net Open Source Initiative - COVIDx CT-3 Dataset

Update 2022-06-02: We released the COVIDx CT-3A and CT-3B datasets, comprising 425,024 CT slices from 5,312 patients and 431,205 CT slices from 6,068 patients, respectively.

Update 2022-03-10: The COVID-Net CT-2 paper was published in Frontiers in Medicine.

Update 2021-01-26: We released the COVID-Net CT-2 models and COVIDx CT-2A and CT-2B datasets, comprising 194,922 CT slices from 3,745 patients and 201,103 CT slices from 4,501 patients respectively. The models and dataset are described in this preprint.

Update 2020-12-23: The COVID-Net CT paper was published in Frontiers in Medicine.

Update 2020-12-03: We released the COVIDx CT-1 dataset on Kaggle.

Update 2020-09-13: We released a preprint of the COVID-Net CT paper.

COVIDx CT-3, an open access benchmark dataset that we generated from several open datasets, comprises 194,922 CT slices from 3,745 patients. We will be adding images over time to improve the dataset.

This dataset is being used to train and validate our models for COVID-19 detection from CT images. Useful dataset code and manipulation tools are available in the COVID-Net CT repository.

Different versions of the dataset may be accessed via the version history, or from the following links: * COVIDx CT-1 * COVIDx CT-2 * COVIDx CT-3

Notably, the "B" variant of the dataset is not provided here due to a more restrictive no-derivatives license. Instructions and scripts for generating the "B" variant of the dataset are available here.

COVIDx CT-3 is released under a CC BY-NC-SA 4.0 license in accordance with the licenses of its constituent datasets. Some subsets of the data have less restrictive licenses (see Data Sources below).

If you find our work useful for your research, please cite: @article{Gunraj2020, author={Gunraj, Hayden and Wang, Linda and Wong, Alexander}, title={COVIDNet-CT: A Tailored Deep Convolutional Neural Network Design for Detection of COVID-19 Cases From Chest CT Images}, journal={Frontiers in Medicine}, volume={7}, pages={1025}, year={2020}, url={https://www.frontiersin.org/article/10.3389/fmed.2020.608525}, doi={10.3389/fmed.2020.608525}, issn={2296-858X} } @article{Gunraj2022, author={Gunraj, Hayden and Sabri, Ali and Koff, David and Wong, Alexander}, title={COVID-Net CT-2: Enhanced Deep Neural Networks for Detection of COVID-19 From Chest CT Images Through Bigger, More Diverse Learning}, journal={Frontiers in Medicine}, volume={8}, pages={729287}, year={2022}, url={https://www.frontiersin.org/articles/10.3389/fmed.2021.729287}, doi={10.3389/fmed.2021.729287}, issn={2296-858X} } Links to the constituent datasets and their respective licenses and citations may be found below under the Data Sources heading.

Core COVID-Net Team

• DarwinAI Corp., Canada and Vision and Image Processing Research Group, University of Waterloo, Canada
  • Linda Wang
  • Alexander Wong
  • Zhong Qiu Lin
  • Paul McInnis
  • Audrey Chung
  • Melissa Rinch
  • Maya Pavlova
  • Naomi Terhljan
  • Siddharth Surana
  • Andy Zhao
  • Hayden Gunraj, COVID-Net for CT
  • Jeffer Peng, COVIDNet UI
• Vision and Image Processing Research Group, University of Waterloo, Canada
  • James Lee
  • Hossein Aboutalebi
  • Alex MacLean
  • Saad Abbasi
• Ashkan Ebadi and Pengcheng Xi (National Research Council Canada)
• Kim-Ann Git (Selayang Hospital)
• Abdul Al-Haimi, COVID-19 ShuffleNet Chest X-Ray Model
• Dr. Ali Sabri (Department of Radiology, Niagara Health, McMaster University, Canada)

Data Structure

COVIDx CT-3 is divided into two variants: "A" and "B". The "A" variant consists of cases with confirmed diagnoses (i.e., RT-PCR, radiologist-confirmed, etc.). The "B" variant ...

Analysis of ‘Indonesia-Coronavirus’ provided by Analyst-2 (analyst-2.ai), based on source dataset retrieved from https://www.kaggle.com/ardisragen/indonesia-coronavirus-cases on 30 September 2021.

--- Dataset description provided by original source is as follows ---

Context

COVID-19 has infected many people in Indonesia, and the number of confirmed cases is increasing exponentially. Indonesia has raised its coronavirus alert to the "Darurat Nasional (National Emergency)" until 29 May 2020. The Java island, especially Jakarta, the capital city of Indonesia, is the most affected region by the coronavirus.

https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F2849532%2Ff46e130bad5d4e74a8835ca057dd05ca%2Facc.png?generation=1584939612835429&alt=media" alt="">

https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F2849532%2F93b53d1b6601da74041f41ea4ba227f6%2Fcases.png?generation=1584938551413887&alt=media" alt="">

Following are the list of available online portals announce the information of COVID-19, from the public community and provincial (regional) government website in Indonesia.

1. https://www.covid19.go.id/situasi-virus-corona/, by Indonesian National Board for Disaster Management.
2. https://kawalcovid19.id/, by Kawal Covid-19 Indonesia community.
3. https://corona.jakarta.go.id/, Jakarta tanggap Covid-19 by Pemda DKI Jakarta.
4. https://pikobar.jabarprov.go.id/, Pusat Informasi & Koordinasi COVID-19, by Pemprov Jawa Barat.
5. https://corona.jatengprov.go.id/, Jawa Tengah Tanggap COVID-19, by Pemprov Jawa Tengah.
6. https://corona.sumbarprov.go.id/, Sumbar Tanggap Corona, by Pemprov Sumatera Barat.
7. http://corona.jogjaprov.go.id/, Yogyakarta Tanggap Covid-19, by Pemprov DIY.
8. https://covid19.bandung.go.id/. Pusat Informasi & Koordinasi COVID-19 Kota Bandung.

We make a structured dataset based on the report materials in these portals. Thus, the research community can apply recent AI and statistical techniques to generate new insights in support of the ongoing fight against this infectious disease in Indonesia.

Current State

Dataset 1) Total Confirmed Positive Cases 2) Google Trend Related keywords 3) Patient Epidemiological Data 4) Daily Case Statistics 5) Case per Province 6) Case in Jakarta Capital City 7) Daily New Confirmed Cases in Each Province (Timeline)

Kernel 1) Predicting Coronavirus Positive Cases in Indonesia 2) Visualization & Analysis of Covid-19 in Indonesia 3) Logistic Model for Indonesia COVID-19 4) DataSet Characteristics of Corona patients in several countries, including Indonesia 5) Novel Corona Virus (Covid-19) Indonesia EDA 6) Simple Visualization and Forecasting 7) Characteristics of Corona patients DS

Related Publication 1) Response to Covid-19: Data Analytics and Transparency, Koderea Talks, 18 March 2020, https://www.researchgate.net/publication/340003505_Response_to_Covid-19_Data_Analytics_and_Transparency 2) Covid-19 Data Science, ID Institute Obrolin Data Coronavirus, 24 March 2020, https://www.researchgate.net/publication/340116231_IDInstitute_Covid-19_Data_Science

Other Country Level Datasets

• South Korea - https://www.kaggle.com/kimjihoo/coronavirusdataset
• Italy - https://www.kaggle.com/sudalairajkumar/covid19-in-italy
• Brazil - https://www.kaggle.com/unanimad/corona-virus-brazil
• USA - https://www.kaggle.com/sudalairajkumar/covid19-in-usa
• France - https://www.kaggle.com/lperez/coronavirus-france-dataset
• Tunisia - https://www.kaggle.com/ghassen1302/coronavirus-tunisia
• Japan - https://www.kaggle.com/tsubasatwi/close-contact-status-of-corona-in-japan

Acknowledgements

Thanks sincerely to all the members of the DSCI Team, KawalCovid19.id, Pemda DKI Jakarta, Pemprov Jawa Barat, Pemprov Jawa Tengah, Pemprov Sumatera Barat, and Pemprov DIY.

DSCI Team

1. Ardiansyah (ardisragen)
2. Tri A Sundara (trilabs)
3. Thomhert (thomhert)
4. Epsi Sayidina (epsisayidina)
5. Teuku Hashrul (hahasrul)
6. Naufal Hakim (hakimbazol)

Invitation

We welcome anyone to join us as collaborators! Join WAG Chat: https://s.id/fgPoP For more information please contact ardi@ejnu.net or WA +8210-4297-0504

Working with https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F2849532%2Fd56eaf0a5d770d756a54cec0d09c87ff%2Fkoderea.png?generation=1584539195622597&alt=media" alt="">

--- Original source retains full ownership of the source dataset ---

This dataset contains records of publicly reported data on COVID-19 testing in Ontario long-term care homes. It was collected between April 24, 2020 and March 30, 2023.

Summary data is aggregated to the provincial level. Reports fewer than 5 are indicated with <5 to maintain the privacy of individuals.

Data includes:

• Long-term care home COVID-19 summary data
• Long-term care homes with an active COVID-19 outbreak
• Long-term care homes no longer in a COVID-19 outbreak
• Long-term care home COVID-19 summary data by Public Health Unit (PHU)
• Long-term care home COVID-19 staff vaccination rates

An outbreak is defined as two or more lab-confirmed COVID-19 cases in residents, staff or other visitors in a home, with an epidemiological link, within a 14-day period, where at least one case could have reasonably acquired their infection in the long-term care home. Prior to April 7, 2021, the definition required one or more lab-confirmed COVID-19 cases in a resident or staff in the long-term care home.

Notes

February 21 to March 29, 2023: Data is only available for regular business days (for example, Monday through Friday, except statutory holidays)

March 12 – 13, 2022: Due to technical difficulties, data is not available.

September 8, 2022: The data dated September 6, 2022 represents data collected during the period of September 3, 4 and 5, 2022.

October 6, 2022: The data dated October 5, 2022 represents data collected during the period of October 1, 2, 3 and 4, 2022.

October 13, 2022: Due to technical difficulties, data for the date of October 9 is not available.

October 20, 2022: Due to technical difficulties, data for the dates of October 15, 16 is not available.

November 24, 2022: Due to technical difficulties, data is not available.

SARS-CoV-2 RNA (N1 and N2 genes) and PMMoV RNA concentrations in primary effluent from the ARA Werdhölzli were determined for the period of September 2020-January 2021. COVID-19 cases in the catchment area are also reported for comparison of RNA concentrations to clinical case data. Data are included in an analysis of COVID-19 disease trajectory overtime.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have originated in Wuhan City, Hubei Province, China, in December 2019. Infection with this highly dangerous human-infecting coronavirus via inhalation of respiratory droplets from SARS-CoV-2 carriers results in coronavirus disease 2019 (COVID-19), which features clinical symptoms such as fever, dry cough, shortness of breath, and life-threatening pneumonia. Several COVID-19 waves arose in Taiwan from January 2020 to March 2021, with the largest outbreak ever having a high case fatality rate (CFR) (5.95%) between May and June 2021. In this study, we identified five 20I (alpha, V1)/B.1.1.7/GR SARS-CoV-2 (KMUH-3 to 7) lineage viruses from COVID-19 patients in this largest COVID-19 outbreak. Sequence placement analysis using the existing SARS-CoV-2 phylogenetic tree revealed that KMUH-3 originated from Japan and that KMUH-4 to KMUH-7 possibly originated via local transmission. Spike mutations M1237I and D614G were identified in KMUH-4 to KMUH-7 as well as in 43 other alpha/B.1.1.7 sequences of 48 alpha/B.1.1.7 sequences deposited in GISAID derived from clinical samples collected in Taiwan between 20 April and July. However, M1237I mutation was not observed in the other 12 alpha/B.1.1.7 sequences collected between 26 December 2020, and 12 April 2021. We conclude that the largest COVID-19 outbreak in Taiwan between May and June 2021 was initially caused by the alpha/B.1.1.7 variant harboring spike D614G + M1237I mutations, which was introduced to Taiwan by China Airlines cargo crew members. To our knowledge, this is the first documented COVID-19 outbreak caused by alpha/B.1.1.7 variant harboring spike M1237I mutation thus far. The largest COVID-19 outbreak in Taiwan resulted in 13,795 cases and 820 deaths, with a high CFR, at 5.95%, accounting for 80.90% of all cases and 96.47% of all deaths during the first 2 years. The high CFR caused by SARS-CoV-2 alpha variants in Taiwan can be attributable to comorbidities and low herd immunity. We also suggest that timely SARS-CoV-2 isolation and/or sequencing are of importance in real-time epidemiological investigations and in epidemic prevention. The impact of G614G + M1237I mutations in the spike gene on the SARS-CoV-2 virus spreading as well as on high CFR remains to be elucidated.