FluView Public Health Laboratory Surveillance

Attribute Details
Source Name fluview_resp_lab_ph
Data Source CDC FluView / Public Health Laboratories
Geographic Levels state, census_division, hhs, nation
Temporal Granularity Weekly for nation, hhs, census_division (week ending Saturday). Seasonal for state (anchored to week 40)
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 and expands the public health laboratory component of legacy V3 fluview_clinical. Subtype counts are organized under dedicated signal names, including Avian Influenza A(H5). See Relationship to V3.

Table of contents

  1. Overview
  2. Indicators (Signals)
  3. Estimation
    1. Metric Definition
    2. Smoothing
    3. Uncertainty
    4. Temporal Handling
    5. Geographic Handling
  4. Relationship to V3
  5. Schema
    1. Columns
  6. Missingness & Privacy
  7. Limitations
  8. Lag & Backfill
  9. Source and Licensing

Overview

Public health laboratories report influenza testing and subtyping results to the CDC through the National Respiratory and Enteric Virus Surveillance System (NREVSS). These laboratories test a subset of positive specimens forwarded from clinical laboratories to identify virus subtypes and lineages.

Delphi ingests this data weekly from the CDC FluView Interactive portal. The dataset tracks circulating strains through specimen counts across nine subtypes and lineages, including A(2009 H1N1), A(H3N2), A(H5), A(H3N2v), B/Victoria, and B/Yamagata.

For diagnostic testing volume and positivity rates from clinical laboratories, see FluView Clinical Labs. For outpatient syndromic surveillance, see FluView ILINet.

Indicators (Signals)

All indicators are weekly or seasonal specimen counts.

Indicator Name Pathogen or Lineage Metric Type Description
total_specimens Influenza Count Total specimens tested by participating public health laboratories.
positive_a_h1n1_2009 Influenza A(H1N1)pdm09 Count Number of specimens positive for pandemic Influenza A(2009 H1N1).
positive_a_h3 Influenza A(H3N2) Count Number of specimens positive for Influenza A(H3N2).
positive_a_h5 Influenza A(H5) Count Number of specimens positive for Influenza A(H5) (Avian Influenza).
positive_a_no_subtype Influenza A Count Number of Influenza A specimens for which subtyping was not performed.
positive_a_h3n2v Influenza A(H3N2v) Count Number of specimens positive for variant Influenza A(H3N2v).
positive_b Influenza B Count Number of Influenza B specimens for which lineage determination was not performed.
positive_b_vic Influenza B (Victoria) Count Number of specimens positive for Influenza B (Victoria lineage).
positive_b_yam Influenza B (Yamagata) Count Number of specimens positive for Influenza B (Yamagata lineage).

Estimation

Metric Definition

All signals are direct counts of subtyped respiratory specimens without rates:

  • For national, HHS, and census division levels (nation, hhs, census_division), counts represent discrete weekly specimen volumes.
  • For the state level (state), counts represent cumulative seasonal totals starting from MMWR week 40.

Smoothing

All signals are unsmoothed discrete specimen counts.

Uncertainty

Uncertainty intervals and standard errors are not published by the CDC for public health laboratory surveillance. The dataset includes total_specimens as a direct measure of characterization 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 (or week 40 for seasonal state data).
  • 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). Because all indicators in this source are additive specimen counts, Delphi reconstructs a combined statewide ny record (fill_method = 'nyc_plus_ny_minus_nyc') when both are reported for a given period.

Raw counts are summed directly:

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

Relationship to V3

This source reproduces and expands the public health laboratory component formerly bundled within the legacy V3 fluview_clinical endpoint and CDC FluView download scripts.

V3 Concept V5 Signal Notes
total_specimens total_specimens Public health lab testing volume
a_2009_h1n1 positive_a_h1n1_2009 Renamed to standard prefix
a_h3 positive_a_h3 Renamed to standard prefix
(not available) positive_a_h5 New in V5. Captures Avian Influenza A(H5)
a_subtyping_not_performed positive_a_no_subtype Renamed to standard prefix
h3n2v positive_a_h3n2v Renamed to standard prefix
b positive_b Renamed to standard prefix
b_vic positive_b_vic Renamed to standard prefix
b_yam positive_b_yam Renamed to standard prefix

What changed in V5:

  • Avian Influenza A(H5) Ingestion. The CDC added A (H5) to the public health laboratory feed to monitor avian influenza spillovers. V5 captures positive_a_h5 as a standard indicator.
  • Dedicated Source Separation. Public health laboratory surveillance is separated from clinical laboratory testing into its own endpoint (fluview_resp_lab_ph).
  • Explicit Geographic Temporal Model. Documents the difference between weekly multi-state levels (nation, hhs, census_division) and seasonal state-level reporting.

Schema

Columns

Column Key Type Data Type Description
signal Primary Key string The name of the indicator (e.g., total_specimens, positive_a_h3, positive_a_h5).
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 Laboratory specimen count.

Missingness & Privacy

  • This source is a voluntary reporting network. If public health laboratories perform no testing within a jurisdiction during a period, that observation is omitted from the dataset rather than recorded as zero.
  • No cell suppression or volume masking is applied.

Limitations

  • Public health laboratories do not test a representative sample of respiratory infections. Specimens are selectively forwarded from clinical laboratories based on severity, unusual presentations, or outbreak investigations. Specimen counts track relative strain prevalence and genetic diversity rather than community incidence.
  • State counts represent cumulative seasonal totals, while national, HHS, and census division counts represent weekly volumes.
  • Due to the global extinction of the Influenza B/Yamagata lineage, positive_b_yam counts are expected to remain near zero in modern seasons.

Lag & Backfill

  • Initial weekly data is published by the CDC on Fridays, six days after the surveillance week ends.
  • Subtyping and genomic sequencing take longer to process than clinical tests. Backfill occurs as laboratories finish sequencing and submit delayed reports. Revisions can be accessed via the /archive/ endpoint or by querying with snapshot_date.

Source and Licensing

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