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Test Menu Details

SARS-CoV-2 & Influenza A/B NAAT with Reflex

Updated2/21/2025
Search TermsCOVID-19; SARS-CoV-2; Influenza A; Influenza B; Flu SC2; COVID-19 Sequencing
How to OrderEach specimen must be accompanied by an approved test order specified by OSPHL.

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.
AvailabilityWith State Acute and Communicable Disease Prevention Program (ACDP) or OSPHL approval only.
PerformedDaily
Time to ReportingWithin 5 working days after receipt of specimen
CPT Code87636

Specimen Collection Details

CollectionThe preferred specimens are clinician-collected nasopharyngeal swab (NP swab), anterior nasal swab, or nasal swab collected by the patient in a healthcare setting.

Use only synthetic fiber swabs with plastic or wire shafts. Place the swab immediately into a sterile container containing 3 mL of viral transport media, universal transport media, or sterile saline.

DO NOT SUBMIT Molecular Transport Media (MTM) for this test. Media containing guanidine thiocyanate or similar chemicals are not acceptable for testing.
Optimal Volume3.0 mL
Minimum Volume1.0 mL
HandlingStore 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 or lower pending transport. Specimens may also be stored 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 calendar days of specimen collection.

If specimen or extract has been frozen, transport using dry ice to maintain frozen temperatures.
Rejection CriteriaSpecimens received more than 7 calendar days after date of collection.

Specimens are subject to the requirements of the OSPHL Specimen Submission Policy (pdf).
CommentsSpecimens received more than 4 days after specimen collection will be tested using the alternate testing method.

When SARS-CoV-2 or influenza are detected, reflex testing may be conducted. For complete details please review the COVID-19 Testing Algorithm (pdf).

State epidemiologists may request additional respiratory pathogen testing or SARS-CoV-2 sequencing from OSPHL if needed for outbreak identification and management.

If laboratory circumstances or reagent supply require, OSPHL may test specimens for this test order using the SARS-CoV-2 & Influenza A/B Multiplex Real-Time RT-PCR test.

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

Method Details

MethodologySARS-CoV-2/Influenza Primary Testing Method:
  • Aptima SARS-CoV-2/Influenza Assay - Nucleic Acid Amplification Test (NAAT) (Entity: Hologic, Inc.)
SARS-CoV-2 & Influenza Testing Alternative Method:
  • Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay - Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) (Entity: Centers for Disease Control and Prevention (CDC))
Performance
Specifications		The Aptima SARS-CoV-2/Influenza testing assay is performed under FDA Emergency Use Authorization. Additional details can be found in the package insert provided by the manufacturer.

The CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex assay is performed as a modification of the procedure under FDA Emergency Use Authorization. Performance Specifications are available on the FDA Emergency Use Authorization webpage.

Change Log

2/21/2025Updated Comments
2/19/2025Updated Search Terms; How to Order; Availability; Handling
5/23/2023Reviewed, no changes