FluView Clinical Laboratory Surveillance

Attribute	Details
Source Name	`fluview_resp_lab_clinical`
Data Source	CDC FluView / Clinical Laboratories
Geographic Levels	`state`, `census_division`, `hhs`, `nation`
Temporal Granularity	Week, ending Saturday
Reporting Cadence	Weekly (Fridays)
Temporal Scope Start	2015-10-10 (2015w40)
Temporal Scope End	Ongoing
Extra Key Columns	None
License	Public Domain US Government

This source reproduces the legacy V3 fluview_clinical endpoint. Signal names follow standard V5 conventions, statewide New York is pooled from NYC and non-NYC components, and public health lab data is now separated into fluview_resp_lab_ph. See Relationship to V3.

Overview
Indicators (Signals)
Estimation
Relationship to V3
Schema
1. Columns
Missingness & Privacy
Limitations
Lag & Backfill
Source and Licensing

Overview

Clinical laboratories in hospitals, commercial reference labs, and clinics report weekly respiratory test results to the CDC through the National Respiratory and Enteric Virus Surveillance System (NREVSS).

Delphi ingests this data weekly from the CDC FluView Interactive portal. The dataset reports laboratory-confirmed influenza test volume, positive results for Influenza A and B, and test positivity rates.

For outpatient syndromic surveillance, see FluView ILINet. For subtyping and lineage data, see FluView Public Health Labs.

Indicators (Signals)

Indicator Name	Pathogen or Disease	Metric Type	Description
`total_specimens`	Influenza	Count	Weekly count of respiratory specimens tested for influenza by participating clinical laboratories.
`positive_a`	Influenza A	Count	Weekly count of specimens testing positive for Influenza A.
`positive_b`	Influenza B	Count	Weekly count of specimens testing positive for Influenza B.
`pct_positive`	Influenza	Percentage	Percentage of tested specimens positive for any influenza virus ($100 \cdot \frac{\text{positive_a} + \text{positive_b}}{\text{total_specimens}}$).
`pct_positive_a`	Influenza A	Percentage	Percentage of tested specimens positive for Influenza A.
`pct_positive_b`	Influenza B	Percentage	Percentage of tested specimens positive for Influenza B.

Estimation

Metric Definition

Overall positivity (pct_positive) is the percentage of tested specimens positive for any influenza virus, dividing combined positive detections (positive_a plus positive_b) by total_specimens and multiplying by 100.
Specific positivity (pct_positive_a, pct_positive_b) is the percentage of tested specimens positive for Influenza A or B, dividing positive_a or positive_b by total_specimens and multiplying by 100.
Counts (total_specimens, positive_a, positive_b) pass through directly from the CDC as raw weekly test volumes and positive detections.

Smoothing

All signals are unsmoothed discrete 7-day weekly totals or ratios.

Uncertainty

Uncertainty intervals and standard errors are not published by the CDC for clinical laboratory surveillance. The dataset includes total_specimens as a direct measure of reporting volume.

Temporal Handling

Observations cover 7-day epidemiological weeks defined by the CDC’s Morbidity and Mortality Weekly Report (MMWR). An MMWR week runs from Sunday through Saturday, standardizing public health reporting across calendar years.

reference_time is the Saturday week-ending date of the surveillance week.
report_time is the release date when Delphi ingested the weekly CDC snapshot. Revisions update past weeks as delayed laboratory reports arrive.

Geographic Handling

All four geographic levels (nation, hhs, census_division, state) are computed natively by the CDC and ingested directly without regional aggregation (fill_method = 'source').

At the state level, the CDC reports New York as two separate jurisdictions: New York City (nyc) and New York State excluding NYC (ny_minus_nyc). When both are reported for a given week, Delphi reconstructs a combined statewide ny record (fill_method = 'nyc_plus_ny_minus_nyc').

Raw counts are summed directly:

\[C_{\text{NY}, t} = C_{\text{NYC}, t} + C_{\text{NY-NYC}, t}\]

where $C$ represents each specimen count (total_specimens, positive_a, positive_b).

Positivity percentages are recomputed as pooled ratios using the summed counts:

\[\text{pct\_positive}_{\text{NY}, t} = 100 \cdot \frac{\text{positive\_a}_{\text{NY}, t} + \text{positive\_b}_{\text{NY}, t}}{\text{total\_specimens}_{\text{NY}, t}}\]

Type-specific positivity percentages (pct_positive_a, pct_positive_b) are recomputed analogously using their respective summed counts.

Relationship to V3

This source reproduces the legacy V3 fluview_clinical endpoint (https://api.delphi.cmu.edu/epidata/fluview_clinical/).

V3 Field	V5 Signal	Notes
`total_specimens`	`total_specimens`	Exact match
`total_a`	`positive_a`	Renamed to standard `positive_*` prefix (Influenza A positive count)
`total_b`	`positive_b`	Renamed to standard `positive_*` prefix (Influenza B positive count)
`percent_positive`	`pct_positive`	Renamed from `percent_` to standard `pct_` prefix
`percent_a`	`pct_positive_a`	Renamed from `percent_` to standard `pct_` prefix
`percent_b`	`pct_positive_b`	Renamed from `percent_` to standard `pct_` prefix

What changed in V5:

Standardized Signal Naming. Positive counts use the positive_* prefix (formerly total_a, total_b), and positivity percentages use the pct_* prefix (formerly percent_*).
Dedicated Source Separation. Clinical laboratory surveillance is separated from public health laboratory testing into its own endpoint (fluview_resp_lab_clinical).

Schema

Columns

Column	Key Type	Data Type	Description
`signal`	Primary Key	string	The name of the indicator (`total_specimens`, `positive_a`, `positive_b`, `pct_positive`, `pct_positive_a`, `pct_positive_b`).
`report_time`	Primary Key	date	The date Delphi ingested the CDC weekly file (`YYYY-MM-DD`).
`geo_type`	Primary Key	string	Geographic level (`state`, `census_division`, `hhs`, `nation`).
`geo_value`	Primary Key	string	Location code.
`fill_method`	Primary Key	string	`source` for directly ingested rows. `nyc_plus_ny_minus_nyc` for reconstructed statewide NY.
`reference_time`	Primary Key	date	Saturday week-ending date of the surveillance week (`YYYY-MM-DD`).
`value`	Value Column	float	Test positivity percentage or specimen count.

Missingness & Privacy

This source is a voluntary reporting network. If no laboratories report within a jurisdiction during a week, that observation is omitted from the dataset rather than recorded as zero.
No cell suppression or volume masking is applied to clinical laboratory testing data.

Limitations

Testing practices vary over time and across facilities. Changes in clinician testing thresholds, adoption of multiplex PCR panels, and institutional guidelines can affect test positivity rates.
Laboratory participation varies across states. Coverage depends on the number and market share of enrolled laboratories in each jurisdiction.
Clinical laboratories differentiate between Influenza A and B, but do not perform genetic subtyping. For subtyping, consult fluview_resp_lab_ph.

Lag & Backfill

Initial weekly data is published by the CDC on Fridays, six days after the surveillance week ends.
Backfill is common during the first two to four weeks as participating laboratories submit delayed reports. Revisions can be accessed via the /archive/ endpoint or by querying with snapshot_date.

Source and Licensing

Clinical laboratory surveillance data is collected by the CDC National Center for Immunization and Respiratory Diseases (NCIRD) via NREVSS. The data is in the public domain.