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Test Menu Details

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

Updated

11/9/2022 (reviewed 5/23/2023)

Search Terms
 COVID-19; SARS-CoV-2; 2019 nCoV; Influenza A; Influenza B; Flu SC2; COVID-19 Sequencing
How to Order

Each specimen must be accompanied by an OSPHL COVID-19 and Influenza Test Request Form used for group or outbreak collections.

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) approval only. Please review the Criteria for COVID-19 Testing at OSPHL (pdf).
Performed

Daily

Time to Reporting

Within 5 working days after receipt of specimen

CPT Code

87636



Specimen Collection Details

Collection

The 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 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 or lower pending transport.  
Transport

Package 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 Criteria
Specimens received more than 7 calendar days after date of collection.

Specimens are subject to the requirements of the OSPHL Specimen Submission Policy and Criteria, available at: http://bit.ly/SpecimenCriteria.
Comments
Specimens 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.

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

Method Details

Methodology

SARS-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

5/23/2023
Reviewed, no changes
11/9/2022Updated COVID-19 and Influenza Testing Algorithm
11/4/2022Review as new. OSPHL implemented use of the Hologic Aptima SARS-CoV-2/Influenza NAAT test. Page content modified to reflect criteria specific to this test.
3/30/2022

Re-Order SARS-CoV-2 Testing Methods for current testing algorithm; Add ClearLabs Clear DxTM for SARS-CoV-2 Sequencing
5/10/2021Changes to Collection, Handling, and Transport to permit submission of RNA extracts by clinical laboratories.
3/26/2021Various changes to support SARS-CoV-2 sequencing implementation. Review the following sections as new: Search Terms, How to Order, Availability, Time to Reporting, Collection, Handling, Comments, Methodology, and Performance Specifications.
3/15/2021

Reviewed; no changes made