Influenza A Subtyping by Sequencing
Test Mnemonic
FLUSEQ
CPT Codes
- 87502 - QTY (1)
- 87503 - QTY (1)
LOINC ®
22827-0
Aliases
- flu genotype
- flu subtype
- flu subtyping
- FLUSEQ
- influenza genotype
- influenza subtype
- influenza subtyping
- SQFLUSEQ
Includes
- Influenza A Subtype
Performing Laboratory
Cleveland Clinic Laboratories
Alternate Specimen Requirements
| Volume | Type | Container | Collect Temperature | Transport Temperature | Special Instructions |
|---|---|---|---|---|---|
| 3 mL | Swab(s) | Saline | Refrigerated | Sterile saline may be used to collect swabs if UTM cannot be sourced. | |
| 1 mL | Swab(s) | E Swab | Refrigerated | E-swabs in liquid amies may be used to collect swabs if UTM cannot be sourced. | |
| 3 mL | Swab(s) | Viral Transport Media | Refrigerated | Viral transport media (including VTM, M4RT, M5, or M6) may be used to collect swabs is UTM cannot be sourced. | |
| 3 mL | Nasal | Universal Transport Media (UTM) | Refrigerated | 1. Insert the entire collection tip of the regular-tip flocked swab with a rigid shaft (i.e. Oracle 1063581) 1/2 - 3/4 of an inch or 1 - 1.5 cm inside the nostril. 2. Firmly sample the nasal wall by rotating the swab in a circular path against the nasal wall at least 4 times. 3. Take approximately 15 seconds to collect the specimen. Be sure to collect any nasal drainage that may be present on the swab. 4. Repeat in the other nostril using the same swab. 5. Place swab, tip first, into the transport tube provided. Break the swab shaft at the score line, discard the top portion of the stem, and close the cap. |
Stability
| Environmental Condition | Description |
|---|---|
| Refrigerated | 7 days |
| Frozen | 30 days |
| Ambient | 24 hours |
Days Performed
Tue, Thu
Turnaround Time
7 days
Methodology
| Name | Description |
|---|---|
| Sequencing |
Clinical Info
Influenza A viruses have segmented single-stranded RNA genomes and are divided into subtypes based on their hemagglutinin (H) and neuraminidase (N) subtypes. Current subtypes of influenza A viruses that routinely circulate in humans and cause seasonal influenza are A(H1N1)pdm09 and A(H3N2). Over 130 influenza A subtype combinations have been identified in other animals, predominantly in wild birds. Genetic reassortment or mutations in these novel influenza A viruses can lead to better adaptation for human infection, and are the basis of flu pandemics. In 2020-2021, a new strain of highly pathogenic avian influenza A(H5N1) virus began affecting wild birds. In the United States, there have been outbreaks with these viruses among poultry and dairy cows, as well as sporadic human infections mostly tied to poultry and dairy cow exposure. In light of the ongoing avian influenza A(H5) virus animal outbreak in the United States, CDC now recommends that all influenza A positive respiratory specimens from hospitalized patients, especially from those in an ICU, be subtyped for seasonal influenza A viruses as soon as possible following admission, to support optimal patient care and proper infection prevention and control measures and to facilitate rapid public health investigation and action. This Influenza A Subtyping by Sequencing assay is a lab-developed test that uses next-generation sequencing technology to sequence the entire influenza A genome, with subsequent analysis using a custom bioinformatic pipeline. This test reports influenza A(H1N1), influenza A(H3N2), or influenza A(H5N1) subtypes only if both hemagglutinin (H) and neuraminidase (N) gene segments are successfully sequenced. Infections with mixed subtypes or reassorted viruses with contributions of non-H/N segments from novel influenza A may not be reliably identified. This test should only be ordered on samples already-positive for influenza A by a nucleic acid amplification test. Sequencing may not be successful in specimens with low viral load.
Clinical Limitation
Infections with mixed subtypes or reassorted viruses with contributions of non-H/N segments from novel influenza A may not be reliably identified. This test should only be ordered on samples already-positive for influenza A by a nucleic acid amplification test. Sequencing may not be successful in specimens with low viral load.
Clinical Reference
Centers for Disease Control Health Alert Network. CDCHAN-00520: Accelerated Subtyping of Influenza A in Hospitalized Patients. 2025 January 16. https://www.cdc.gov/han/2025/han00520.html.