Public Health Division

Test Menu Details

Influenza SARS-CoV-2 Multiplex Real-Time RT-PCR
Updated	10/29/2026
Search Terms	COVID-19; Influenza A; Influenza B; Flu SC2; Subtyping; H5N1; Avian Flu; Surveillance
How to Order	On the Virology/Immunology Test Request Form (OHA0042), in the "Molecular" section, check the box for "COVID-19: SARS-CoV-2, RT-PCR or NAAT." Complete all required fields. 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. With State Acute and Communicable Disease Prevention Program (ACDP) approval. 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 lab assays; and 3) Respiratory outbreaks.
Performed	Once per week or more, depending on demand
Time to Reporting	Within 5 working days after receipt of specimen
Public Health Data	All data shared are de-identified. Influenza specimens: 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. SARS-CoV-2 specimens: Representative SARS-CoV-2 specimens are referred to CDC's National SARS-CoV-2 Strain Surveillance (NS3) program.
CPT Code	87636

Specimen Collection Details
Collection	Collect specimen(s) using Dacron polyester tips or flocked swabs on a plastic shaft (wooden shaft swabs are not acceptable). Insert swabs into viral transport media (preferred). Universal transport media and sterile saline are acceptable. 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. Acceptable specimen sources include: Upper Respiratory: Nasopharyngeal swabs (preferred), nasal swabs, throat swabs, combination swabs (2 swabs from accepted specimen sources in one vial), nasal aspirates, nasal washes Lower respiratory: bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates. Instructions for collecting respiratory specimens are available at: https://www.cdc.gov/flu-resources/media/pdfs/2024/08/flu-specimen-collection-guide.pdf. 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.
Optimal Volume	3.0 mL
Minimum Volume	1.0 mL
Handling	Store specimens at refrigerated temperatures (2-8°C) pending transport. Specimens that will not be tested within 72 hours of collection should be frozen at -70°C pending transport. Specimens may also be stored at -20°C for up to 3 days. Minimize the potential for multiple freeze/thaw cycles during handling, storage, and testing to prevent viral degradation.
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, transport using dry ice to maintain frozen temperatures during transport.
Rejection Criteria	Dry swabs; swabs containing calcium alginate, cotton tips, or wooden shafts; and specimens submitted in the incorrect transport media. Specimens are subject to the requirements of the OSPHL Specimen Submission Policy (pdf).
Comments	Qualifying specimens may be reflexed to additional testing. Discrepant results between test platforms may occur for specimens containing low quantity of virus. For additional details about OSPHL's testing process, please review the Respiratory Virus Testing Algorithm (pdf). SARS-CoV-2 Positive Specimens: Qualifying specimens may be selected for next generation sequencing for surveillance. For more detail, review the SARS-CoV-2 Next Generation Sequencing Test Menu page. Influenza Positive Specimens: Specimens that test positive for influenza A will be reflexed to Influenza A subtyping assays. For more details refer to the Influenza A and B Real-Time RT-PCR with Reflex Subtyping and Lineage Test Menu page. State epidemiologists may request additional respiratory pathogen testing or SARS-CoV-2 sequencing from OSPHL if needed for outbreak identification and managementt. If laboratory circumstances or reagent supply require, OSPHL may test specimens using alternate methodologies. Original material submitted for testing is retained for 7 calendar days after receipt at the laboratory.

Method Details
Methodology	Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay - Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) (Entity: Centers for Disease Control and Prevention) Modified FDA-cleared, CDC-developed
Performance Specifications	Performance specifications are available here: https://pubmed.ncbi.nlm.nih.gov/34152951/ https://www.accessdata.fda.gov/cdrh_docs/reviews/K190302.pdf

Change Log
10/29/2026	Comprehensive changes; review as new
10/31/2025	Updated Availability
2/21/2025	Updated Comments
2/19/2025	Updated Search Terms; How to Order; Handling; Added Public Health Data