Data Submission Guide¶

Version 2.0.0 (updated 2026-05-18)

Added guidance for the expanded disease set now supported by the reporting standards.
Updated aggregation expectations for newly supported diseases and their applicable dimensions.
Aligned submission guidance with current metadata and validation references.

This guide provides detailed specifications for health departments participating in the US Disease Tracker project to contribute reportable disease count data. To date, this project is seeking data only from jurisdictions already sending case notification data through NNDSS.

Reportable Data Specifications¶

Time Period¶

Start Date: December 29, 2024 (start of MMWR week 1, 2025)
End Date: Through present

Time Aggregation¶

Disease	Weekly
Measles	✓
Pertussis	✓
Invasive Meningococcal Disease	✓
Hepatitis A	✓
Acute Hepatitis B	✓
Perinatal Hepatitis B	✓
Mumps	✓
Mpox	✓
Varicella	✓
Influenza-Associated Pediatric Mortality	✓

Confirmation Status¶

Required confirmation status by disease:

Disease	Confirmation Status
Measles	Confirmed only
Pertussis	Confirmed and probable combined
Invasive Meningococcal Disease	Confirmed and probable combined
Hepatitis A	Confirmed only
Acute Hepatitis B	Confirmed and probable combined
Perinatal Hepatitis B	Confirmed only
Mumps	Confirmed and probable combined
Mpox	Confirmed and probable combined
Varicella	Confirmed and probable combined
Influenza-Associated Pediatric Mortality	Confirmed only

Required Data Stratifications¶

Disease counts for different breakdowns are collected separately (e.g., age, sub-jurisdiction, disease subtype, etc.). We call these versions of the data the "data stratifications". Each data stratification should provide complete data from December 29, 2024 through the present, with each having equivalent total counts over time (e.g., cumulative measles cases in the age group stratification must equal cumulative measles cases in the sub-jurisdiction stratification). For each stratification, the counts by time period (i.e., week, cumulative) should sum to the equivalent time period for the full jurisdication (e.g., the sum of county-level cases of measles for state Y should equal the number of total cases in state Y for all time points); data suppression should not result in underreporting through use of "unspecified" strata (see Data Suppression). See Case Classification by Time below for details on assignment of cases to time periods. Only the data stratifications listed below will be accepted; new stratifications will be added as needed for new demographics, diseases, conditions or outcomes, etc.

Important

All stratifications must sum to the same count (by time period and total). This sum should be equivalent to the jurisdication-level count for that time period. Do not drop counts in reporting. Follow Data Suppression instructions to ensure complete reporting.

Data Stratifications:¶

Measles
- Cases × week × sub-jurisdiction unit (county, planning area, sub-state region, etc.)
- Cases × week × age group × jurisdiction (state, DC, NYC, or territory)

Pertussis
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Invasive Meningococcal Disease
- Cases × week × sub-jurisdiction unit 
- Cases × week × age group × jurisdiction 
- Cases × week × serogroup × jurisdiction

Hepatitis A
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Acute Hepatitis B
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Perinatal Hepatitis B
- Cases × week × sub-jurisdiction unit

Mumps
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Mpox
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Varicella
- Cases × week × sub-jurisdiction unit
- Cases × week × age group × jurisdiction

Influenza-Associated Pediatric Mortality
- Deaths × week × sub-jurisdiction unit
- Deaths × week × age group × jurisdiction

Note: Sub-jurisdiction or age group counts

For conditions where stratified counts by sub-jurisdiction or age group are not feasible due to small numbers or other reasons, jurisdiction-level (e.g., state-level) reporting can be accomplished by using the "unspecified" value for geo_name or age_group. See Data Technical Specifications for details.

Reporting Frequency¶

Data should be reported weekly by Thursday during non-emergency periods. Data can also be uploaded on any other day, but will not be updated on USDT until the next Friday. For each data submission, complete data for all diseases should be included, even if there are no updates.

Note: During large outbreaks or public health emergencies, more frequent updates may be requested to improve situational awareness.

Case Classification by Time¶

Cases should be classified in time according to a hierarchical date algorithm.

Recommended: Use the Calculated Case Counting Date (CCCD)

See CSTE Data Standardization Guidelines for details.

The CCCD employs a hierarchy and assigns the case to the earliest of:

  1. Symptom onset date
  2. Clinical diagnosis date
  3. Earliest specimen collection date associated with a positive lab result
  4. Earliest result date for a positive lab result
  5. Date first received by a public health agency
  6. Date entered/record initiated

Alternative: If CCCD is not implemented, use a similar hierarchical algorithm or an existing case classification date such as Event Date in your system.

Required: Provide metadata on the algorithm used by your jurisdiction.

Time Period Assignment¶

Weekly counts: Classify by MMWR week (see MMWR week table)

Geographic Assignment¶

Cases should be included in aggregated counts according to their place of residence, in accordance with standard epidemiologic practice in the US (see CSTE Position Statement 11-SI-04).

Sub-jurisdiction Reporting¶

Sub-jurisdiction level reporting (below state, territory, or city level) is optimal to maximize usefulness for preparedness and response.

County-level reporing is preferred, but alternate aggregations (region, HSA, etc.) are acceptable.
Each jurisdiction should decide the geographic unit to use and provide a list of geographic units as metadata

Age Groups¶

Age groups are defined to be relevant to both disease epidemiology and vaccine schedules. The same age groupings are used for all diseases to simplify visualizations.

Age Group	Description
<1 y	From birth up to but not including 1 year birthday
1-4 y	From 1 year birthday up to but not including 5 year birthday
5-11 y	From 5 year birthday up to but not including 12 year birthday
12-18 y	From 12 year birthday up to but not including 19 year birthday
19-22 y	From 19 year birthday up to but not including 23 year birthday
23-44 y	From 23 year birthday up to but not including 45 year birthday
45-64 y	From 45 year birthday up to but not including 65 year birthday
>=65 y	From 65 year birthday and older
total	Total counts, all ages
unknown	Counts of individuals with unknown age
unspecified	Aggregated counts of individuals from age groups being suppressed

Important

Age groups will only be shared and displayed at the jurisdiction level, not at sub-jurisdiction level, unless otherwise agreed to by individual jurisdictions.

Data Elements¶

For complete field definitions, data types, valid values, and detailed validation rules, see the Data Technical Specifications.

Summary of Required Fields¶

All data submissions must include the following types of information:

Time fields: When the cases occurred (report period dates and time unit)
Disease fields: What disease is being reported, case confirmation status, and outcome
Geographic fields: Where the cases occurred (jurisdiction and geographic unit)
Count field: Number of cases for this combination
Demographic fields: Age group (for age-stratified aggregations)

Summary of Optional Fields¶

disease_subtype: For meningococcal serogroup reporting.

For detailed specifications of each field including exact field names, data types, and valid value sets, see the Data Technical Specifications.

International Residents¶

International residents (residents of countries outside the US but who had a case identified in that jurisdiction) can be included in reported data. These counts will be excluded from displayed totals and epidemic curves for stratifications and jurisdiction totals. To ensure they are included correctly:

Designate as "international resident" using:
geo_name = "international resident"
geo_unit = "NA"

Data Lags and Incompleteness¶

Jurisdictions should share all cases as soon as they are adjudicated as confirmed or probable, and are ready for public release
The project team recognizes that data from recent weeks is likely to be incomplete but encourages as timely submission of data as possible
The project team will not censor data reported by jurisdictions will display data as they are reported
The project team will clearly indicate provisional data according to jurisdiction guidance through:
- Dashed lines on epidemic curves
- Asterisks and notes detailing data completeness limitations

Data Suppression¶

Small Count Suppression¶

Jurisdictions should use their existing policies regarding suppression of small numerators or where underlying populations are small enough to risk reidentification. All data should have suppression applied by the jurisdiction prior to submission, in accordance with their institutional policies. To ensure clear understanding of the data and transparency, jurisdictions should share applicable documentation of small count suppression policies with the project team if possible.

Handling Suppressed Data¶

To ensure total counts add to 100% of cases:

All cases that cannot be assigned to specific values (i.e., counties, age groups) should be aggregated in an "unspecified" category for that variable.
All other non-suppressed cases should be assigned to their appropriate values.
Allocation of suppression rules and "unspecified" aggregation must be performed prior to data transfer/submission.
Suppression rules should be shared with the project team for accurate description/footnoting.

Example

A jurisdiction with a suppression rule that requires suppression of any count <5, records 31 total cases of measles during a week. County A has 1 case, County B has 3 cases, County C and D have 12 and 15 cases, respectively. For the county-level aggregation of these counts, these should be reported as:

Include a row for each geo_name = "County C" and geo_name = "County D" with count = 12 and count = 15.
Include a row with geo_name = "unspecified" and a value in count that sums all suppressed county counts for this week. In this case count = 4.
Do not include a row for geo_name = "County A" or geo_name = "County B".

Measles Exception¶

For measles, the project team recommends not suppressing data as a default and releasing any cases that have already been publicly released. This is to ensure comparability with counts being produced through various "web-scraping" efforts that exist, which often capture cases reported individually through press releases. Individual requests to suppress data can be discussed with the project team.

Data Format¶

No Zero Reporting¶

Report only non-zero counts (i.e., do not include rows in data where the count equals 0)
For example, if an age group had no reported outcome during a timeframe, no entry is required (e.g., if age group >= 65 has 0 cases of measles for that week for a state, do not include a row with count = 0 for age_group = ">=65")
If a jurisdiction had no reported counts of any disease or outcome during a timeframe, they should still submit the data, even if it has no new additional rows since the prior week's submission. This will enable us to limit missingness and uncertainty in the data.
The database system will automatically add 0s at higher spatial aggregations

File Format¶

Data should be submitted in CSV format following the standard template structure.

Template and Example Files:

Data submission template - Empty template with correct field structure
Example data file - Sample data demonstrating proper format
Jurisdiction specification example - Example format for sharing sub-jurisdiction geographies, particularly for jurisdictions reporting geographies other than county.

File Submission Requirements:

Submit a file with all incident disease counts since December 29, 2024
Each submission should include all updates to current and prior data, with new rows for new time periods
Files will be date-stamped by the system for version control
Changes to prior observation counts will be taken as revisions

File Naming: Jurisdictions should name files following the pattern:

disease_tracking_report_{jurisdiction}_{report_date}.csv

Example: disease_tracking_report_CA-SIMULATED-EXAMPLE_2026-02-09.csv

See the Data Transfer Guide for technical details on data submission methods and the Data Technical Specifications for complete field requirements.

Metadata Requirements¶

Jurisdictions should provide accompanying metadata using the Jurisdiction Reporting Metadata Template. For specifics on metadata, see Data Technical Specifications. Metadata required includes:

Algorithm used to classify cases in time (e.g., CCCD or alternative)
List of substate geographic units used by jurisdiction
Data suppression policies and rules
Any jurisdiction-specific notes or caveats

Validation¶

All submitted data must meet validation requirements to ensure data quality and consistency.

What is validated:

Field formats and data types
Values are within acceptable ranges and valid value sets
Logical consistency across fields
Required fields are present

Resources:

Data Technical Specifications - Complete field definitions and valid value sets
Data dictionary (CSV) - Reference table of all fields and valid values
Validation Rules - Comprehensive validation requirements

Values submitted must align with valid value sets. Values not in alignment may result in validation errors. The Data Transfer Guide describes what happens when validation succeeds or fails.

Questions¶

For questions about data submission requirements, contact the project team.