Daily count of NYC residents who tested positive for SARS-CoV-2, who were hospitalized with COVID-19, and deaths among COVID-19 patients.

Note that this dataset currently pulls from https://raw.githubusercontent.com/nychealth/coronavirus-data/master/case-hosp-death.csv on a daily basis.

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

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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

This dataset contains information on antibody testing for COVID-19: the number of people who received a test, the number of people with positive results, the percentage of people tested who tested positive, and the rate of testing per 100,000 people, stratified by modified ZIP Code Tabulation Area (ZCTA) of residence. Modified ZCTA reflects the first non-missing address within NYC for each person reported with an antibody test result. This unit of geography is similar to ZIP codes but combines census blocks with smaller populations to allow more stable estimates of population size for rate calculation. It can be challenging to map data that are reported by ZIP Code. A ZIP Code doesn’t refer to an area, but rather a collection of points that make up a mail delivery route. Furthermore, there are some buildings that have their own ZIP Code, and some non-residential areas with ZIP Codes. To deal with the challenges of ZIP Codes, the Health Department uses ZCTAs which solidify ZIP codes into units of area. Often, data reported by ZIP code are actually mapped by ZCTA. The ZCTA geography was developed by the U.S. Census Bureau. These data can also be accessed here: https://github.com/nychealth/coronavirus-data/blob/master/totals/antibody-by-modzcta.csv Exposure to COVID-19 can be detected by measuring antibodies to the disease in a person’s blood, which can indicate that a person may have had an immune response to the virus. Antibodies are proteins produced by the body’s immune system that can be found in the blood. People can test positive for antibodies after they have been exposed, sometimes when they no longer test positive for the virus itself. It is important to note that the science around COVID-19 antibody tests is evolving rapidly and there is still much uncertainty about what individual antibody test results mean for a single person and what population-level antibody test results mean for understanding the epidemiology of COVID-19 at a population level.
These data only provide information on people tested. People receiving an antibody test do not reflect all people in New York City; therefore, these data may not reflect antibody prevalence among all New Yorkers. Increasing instances of screening programs further impact the generalizability of these data, as screening programs influence who and how many people are tested over time. Examples of screening programs in NYC include: employers screening their workers (e.g., hospitals), and long-term care facilities screening their residents.

In addition, there may be potential biases toward people receiving an antibody test who have a positive result because people who were previously ill are preferentially seeking testing, in addition to the testing of persons with higher exposure (e.g., health care workers, first responders)

Rates were calculated using interpolated intercensal population estimates updated in 2019. These rates differ from previously reported rates based on the 2000 Census or previous versions of population estimates. The Health Department produced these population estimates based on estimates from the U.S. Census Bureau and NYC Department of City Planning.

Antibody tests are categorized based on the date of specimen collection and are aggregated by full weeks starting each Sunday and ending on Saturday. For example, a person whose blood was collected for antibody testing on Wednesday, May 6 would be categorized as tested during the week ending May 9. A person tested twice in one week would only be counted once in that week. This dataset includes testing data beginning April 5, 2020.

Data are updated daily, and the dataset preserves historical records and source data changes, so each extract date reflects the current copy of the data as of that date. For example, an extract date of 11/04/2020 and extract date of 11/03/2020 will both contain all records as they were as of that extract date. Without filtering or grouping by extract date, an analysis will almost certainly be miscalculating or counting the same values multiple times. To analyze the most current data, only use the latest extract date. Antibody tests that are missing dates are not included in the dataset; as dates are identified, these events are added. Lags between occurrence and report of cases and tests can be assessed by comparing counts and rates across multiple data extract dates.
For further details, visit: • https://www1.nyc.gov/site/doh/covid/covid-19-data.page • https://github.com/nychealth/coronavirus-data • https://data.cityofnewyork.us/Health/Modified-Zip-Code-Tabulation-Areas-MODZCTA-/pri4-ifjk

Results of sampling to determine the SARS-CoV-2 N gene levels in NYC DEP Wastewater Resource Recovery Facility (WRRF) influent, disaggregated by the WRRF where the sample was collected, date sample was collected, and date sample was tested.

RT-qPCR was changed to digital PCR in April of 2023, resulting values are about 10-20 times higher than those of RT-qPCR. Please refer to this supporting documentation for more technical information

Data may be used to track trends in SARS-CoV-2 concentrations in NYC WRRF influent. Dataset does not include COVID-19 case rates.

The table summarizes CFRcrude for each country region at the time of the report, calculated CFRactual and IFR values through early May 2020. Details are available in the cited references [2, 4, 6–14, 16, 19, 21–24, 32, 33, 40, 41]. For the USA and UK the CFRcrude on April 15, 2020 is listed. Studies are listed by their first author or by the location of the modeling group that reported them.

These tables will stop being updated after June 1, 2023. COVID-19 vaccination reporting is expected to resume when a new COVID-19 vaccination formulation is authorized. As 4/22/2023, CDC recommends bivalent vaccine for everyone regardless of age and whether or not the person has had prior monovalent vaccine. This table shows the cumulative number and percentage of people who have received an updated (bivalent) COVID-19 vaccination by race/ethnicity and age group for people 5 years and over. • Data are reported weekly on Thursday and include doses administered to Saturday of the previous week. • All data in this report are preliminary. Data for previous weeks may be changed because of delays in reporting, deduplication, or correction of errors. • The table groups people based on their current age and excludes people known to be deceased. • The analyses here are based on data reported to CT WiZ which is the immunization information system for CT. Connecticut COVID-19 Vaccine Program providers are required to report to CT WiZ all COVID-19 doses administered in CT including to CT residents and to residents of other jurisdictions. CT Wiz also receives records on CT residents vaccinated in other jurisdictions and by federal entities which share data with CT WiZ electronically (currently: RI, NJ, New York City, DE, Philadelphia, NV, Indian Health Service, Department of Veterans Affairs (doses administered since 11/2022)). Electronic data exchange is being added jurisdiction-by-jurisdiction. Once a jurisdiction is added to CT WiZ, the records for residents of that jurisdiction vaccinated in CT are removed. For example, when CT residents vaccinated in NYC were added, NYC residents vaccinated in CT were removed. • Population size estimates used to calculate cumulative percentages are based on 2020 DPH provisional census estimates*. • Race and ethnicity data may be self-reported or taken from an existing electronic health care record. Reported race and ethnicity information is used to create a single race/ethnicity variable. People with Hispanic ethnicity are classified as Hispanic regardless of reported race. People with a missing ethnicity are classified as non-Hispanic. People with more than one race are classified as multiple races. A vaccine coverage percentage cannot be calculated for people classified as NH (non-Hispanic) Other race or NH Unknown race since there are no population size estimates for these groups. Data quality assurance activities suggest that in at least some cases NH Other may represent a missing value. Vaccine coverage estimates in specific race/ethnicity groups may be underestimated as result of the classification of records as NH Unknown Race or NH Other Race. • Cumulative percentage estimates have been capped at 100%. Observed percentages may be higher than 100% for multiple reasons, inaccuracies in the census denominators or reporting errors. DPH Provisional State and County Characteristics Estimates April 1, 2020. Hayes L, Abdellatif E, Jiang Y, Backus K (2022) Connecticut DPH Provisional April 1, 2020, State Population Estimates by 18 age groups, sex, and 6 combined race and ethnicity groups. Connecticut Department of Public Health, Health Statistics & Surveillance, SAR, Hartford, CT.