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Lab Test Details

Influenza Type A and B, Qualitative Real-Time RT-PCR with Reflex IA Subtyping

Updated2/21/2025
Search TermsFlu A and B PCR; Flu A subtyping; H5N1; Avian Flu
How to OrderOn the Virology/Immunology Test Request Form (OHA0042), in the "Molecular" section, check the box for "Influenza RT-PCR Screen."

If the specimen is associated with an identified outbreak, include the outbreak number in the Outbreak Number box on the test request form.

Influenza A subtyping and influenza B genotyping may be reflexed when results are positive for influenza on the SARS-CoV-2 & Influenza Multiplex Real-Time RT-PCR or SARS-CoV-2 & Influenza NAAT tests.
AvailabilityAll clients with approval from the Acute and Communicable Disease Prevention Program (ACDP)

Contact ACDP at 971-673-1111 with notification and/or approval to test for the following: 1) Patients with risk factors for or suspected to be infected with avian or novel influenza; 2) Specimens testing negative on seasonal influenza subtyping or displaying atypical features on atypical lab assays.
PerformedOnce per week or more, depending on demand
Time to ReportingWithin 7 working days after receipt of specimen
Public Health DataData from influenza testing are shared with the Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) as part of Global Influenza Surveillance. https://www.cdc.gov/fluview/?CDC_AAref_Val=https://www.cdc.gov/flu/weekly/fluactivitysurv.htm
CPT Code87502 x 2
If Influenza A is detected, additionally 87503 x 3 (H3, H1N1 (2009) pdm InfA, and HIN1 (2009) pdm H1)

Specimen Collection Details

CollectionCollect specimen(s) using Dacron polyester tips or flocked swabs on a plastic shaft (wooden shaft swabs are not acceptable). Ideally, collect specimens within 3 days of illness onset and not later than 7 days after illness onset. Insert swabs into viral transport media (preferred). Universal transport media and sterile saline are accepted. Do not submit a dry swab for testing.

DO NOT SUBMIT Molecular Transport Media (MTM) for this test. Media containing guanidine thiocyanate or similar chemicals are not acceptable for testing. This media inactivates the virus and cannot be used for all public health surveillance.

Acceptable respiratory specimen sources include:
  • Upper Respiratory: Nasopharyngeal swabs, nasal swabs, throat swabs, combination swabs (2 swabs from accepted specimen sources in one vial)
  • Lower Respiratory: Nasal aspirates, nasal washes, bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates
For people with conjunctivitis with suspected influenza A(H5N1) submit the following two specimens:
  • One nasopharyngeal specimen in viral or universal transport media and one conjunctival swab in viral or universal transport media. OR
  • One nasal swab and one throat swab in a single viral or universal transport media tube and one conjunctival swab in viral transport media.
See the CDC tool for conjunctival swab specimen collection (pdf) for collection guidance.

Conjunctival specimen testing will only be conducted with a paired respiratory specimen. Conjunctival specimens and the paired respiratory specimen will be forwarded to CDC for testing pending verification of the specimen source by OSPHL.

Instructions for collecting respiratory specimens are available at: https://www.cdc.gov/flu-resources/media/pdfs/2024/08/flu-specimen-collection-guide.pdf
Optimal Volume3 mL per tube
Minimum Volume1 mL per tube
HandlingStore specimens at refrigerated temperatures (2-8°C) pending transport.

If specimen transport cannot occur within 2-3 days of specimen collection, freeze the specimen(s), preferably at -70° C, and ship on dry ice as soon as possible. Specimens may also be stored frozen at -20° C for up to 3 days.
TransportPackage specimens with fully frozen ice packs to maintain refrigerated temperatures during transport. Transport for receipt at the OSPHL within 3 days of specimen collection.

If specimen is frozen, package specimens with dry ice to maintain frozen temperatures during transport.
Rejection CriteriaSwabs with calcium alginate, cotton tips, or wooden shafts; specimens that are collected more than 14 days after illness onset.

Specimens are subject to the requirements of the OSPHL Specimen Submission Policy (pdf).
CommentsSpecimens that are positive for influenza A on the SARS-CoV-2 & Influenza Multiplex Real-Time RT-PCR or SARS-CoV-2 & Influenza NAAT tests will have influenza subtyping ordered. Discrepant results between testing platforms may occur for specimens with low quantity or low quality of viral RNA. For additional details about OSPHL's testing process, please review the COVID-19 and Influenza Testing Algorithm (pdf).

This test will identify influenza A (H3, 2009 H1N1, and H3N2v subtypes). Highly pathogenic avian influenza testing (e.g., H5 and H7) available upon ACDP approval. Influenza A subtyping assay result guidance is provided in the Influenza A Subtyping Results Interpretation Table (pdf).

Specimens for people exposed to animals with confirmed Influenza A(H5) will first be tested with the CDC Human Influenza Virus Real-Time Diagnostic Panel Influenza A/H5 Subtyping  test. If this A/H5-specific test is negative (undetected), testing may reflex to  SARS-CoV-2 & Influenza A /B Multiplex Subtyping Real-Time RT-PCR or Influenza A Subtyping Real-Time RT-PCR testing.

OSPHL positive (reactive) results for the Influenza A/H5 test are considered presumptive positive and must be confirmed by the Centers for Disease Control and Prevention (CDC) laboratory. 

OSPHL no longer performs Influenza B lineage/genotyping. Influenza B is assumed to be B Victoria lineage, as B Yamagata lineage has not been detected since March 2020.

If laboratory circumstances or reagent supply require, OSPHL may test specimens for this test order using the SARS-CoV-2 & Influenza A/B NAAT with Reflex test.

Original material submitted for testing is retained for 7 calendar days after receipt at the laboratory.

Method Details

MethodologyReal-Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR)
Performance
Specifications
Method Performance Specifications determined by the Centers for Disease Control and Prevention (CDC). Please contact the CDC for specifications if needed.

Change Log

2/21/2025Updated Comments
1/30/2025Updated Title, Search Terms, Availability, Public Health Data URL, CPT Code, Collection, Handling, Comments
5/31/2024Updated Collection section
4/24/2024Update Search Terms, Collection, Comments for 2024 H5N1 considerations
10/19/2023Updated Collection section
5/23/2023Reviewed; no changes