Public Health Division

Lab Test Details

Influenza Type A and B, Qualitative Real-Time RT-PCR with Reflex IA Subtyping
Updated	10/29/2026
Search Terms	Flu A and B PCR; Flu A subtyping; H5N1; Avian Flu; Swine flu; Bird flu; Atypical flu; unsubtypeable; H3N2 variant
How to Order	On 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. Laboratories submitting specimens for public health surveillance may complete the Respiratory Virus Surveillance Requisition Line List (xlsx / pdf).
Availability	1. Laboratories submitting specimens for influenza or SARS-CoV-2 surveillance. 2. All 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.
Performed	Once per week or more, depending on demand
Time to Reporting	Within 7 working days after receipt of specimen
Public Health Data	Influenza A subtyping data are shared with OHA Partners and Centers for Disease Control and Prevention (CDC) influenza surveillance. Oregon Surveillance Data National Surveillance Data Representative influenza specimens are forwarded to a CDC National Influenza Reference Center (NIRC) for further characterization. Data from these studies are shared with World Health organization (WHO) as part of Global Influenza Surveillance.
CPT Code	87502 x 2 If Influenza A is detected, additionally 87503 x 3 (H3, H1N1 (2009) pdm InfA, and HIN1 (2009) pdm H1)

Specimen Collection Details
Collection	Collect 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), nasal washes, nasal aspirates Lower Respiratory: Bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates For people with suspected influenza A (H5N1) submit the following specimens: No Conjunctivitis One nasopharyngeal swab in VTM or UTM, AND One nasal swab and one throat swab submitted in the same vial of VTM or UTM. With Conjunctivitis One nasopharyngeal swab in VTM or UTM, AND At least one conjunctival swab in VTM or UTM. 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 Volume	3 mL per tube
Minimum Volume	1 mL per tube
Handling	Store 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.
Transport	Package 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 Criteria	Swabs 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).
Comments	Specimens that are positive for influenza A on the SARS-CoV-2 & Influenza Multiplex Real-Time RT-PCR or BioFire RP 2.1 tests will be reflexed to influenza subtyping. 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 Respiratory Virus Testing Algorithm (pdf). These tests 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 assay. If this A/H5-specific test is negative (undetected), testing may reflex to Influenza SARS-CoV-2 Multiplex Subtyping Real-Time RT-PCR. 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 alternate methodologies. Original material submitted for testing is retained for 7 calendar days after receipt at the laboratory.

Method Details
Methodology	Real-Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) Modified FDA-cleared, CDC-developed
Performance Specifications	Method Performance Specifications determined by the Centers for Disease Control and Prevention (CDC). Please contact the CDC for specifications if needed. https://www.accessdata.fda.gov/cdrh_docs/reviews/K243931.pdf

Change Log
10/29/2026	Changes made throughout; review as new
10/31/2025	Updated How to Order, Availability
2/21/2025	Updated Comments
1/30/2025	Updated Title, Search Terms, Availability, Public Health Data URL, CPT Code, Collection, Handling, Comments
5/31/2024	Updated Collection section
4/24/2024	Update Search Terms, Collection, Comments for 2024 H5N1 considerations