Skip to main content

Oregon State Flag An official website of the State of Oregon » Homepage

Lab Test Details

Influenza Type A and B, Qualitative Real-Time RT-PCR

with Reflex Subtyping & Lineage



Search Terms
Flu A and B PCR; Flu A subtyping; Flu B genotyping; Flu B lineage; H5N1
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.

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.
All clients with approval from the Acute and Communicable Disease Prevention Program (ACDP)
PerformedOnce per week or more, depending on demand
Time to ReportingWithin 7 working days after receipt of specimen
Data Sharing
Data 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.
CPT Code87502 x 2
If Influenza A is detected, additionally 87503 x 3 (H3, H1N1 (2009) pdm InfA, and HIN1 (2009) pdm H1).
If Influenza B is detected, additionally 87503 x 2 (Victoria and Yamagata lineage)

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.

For patients suspected of infection with influenza A(H5N1), specimens must be submitted in viral transport media.

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 (preferred), 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:
  1. One nasopharyngeal specimen in viral transport media, and
  2. One conjunctival swab in viral transport media.
Conjunctival specimen testing will only be conducted with a paired respiratory specimen. Conjunctival specimens and the paired NP specimen will be forwarded to CDC for testing pending verification of the specimen source by OSPHL. 

Instructions for collecting respiratory specimens are available at:

Optimal Volume3 mL per tube
Minimum Volume
1 mL per tube

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.
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 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 and Criteria, available at:
Comments Specimens that are positive for influenza A or influenza B on the SARS-CoV-2 & Influenza Multiplex Real-Time RT-PCR or SARS-CoV-2 & Influenza NAAT tests will have influenza subtyping or genotyping automatically 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), and influenza B Victoria and Yamagata lineages. 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. 

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

Method Details


Real-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

Updated Collection section
Update Search Terms, Collection, Comments for 2024 H5N1 considerations
Updated Collection section
Reviewed; no changes
Updated COVID-19 and Influenza Testing Algorithm
11/4/2022Add Data Sharing section; Clarify Collection details; Review Comments as new due to number of changes

Edit Comments and Performance Specifications