Health Update: Guidance for Influenza Testing and Subtyping

Date: October 9, 2026

This is a Provider Alert from Whatcom County Health and Community Services with updated guidance about influenza testing and subtyping for novel influenza viruses.

Current Situation

Emergency Department visits for influenza are currently rising in Washington, indicating an early start to the 2026-2027 influenza season. Providers should be alert for patients with seasonal as well as novel influenza viruses such as highly pathogenic avian influenza (HPAI).

The Centers for Disease Control and Prevention (CDC) and the Association of Public Health Laboratories (APHL) have issued updated surveillance testing recommendations (PDF) for this influenza season. Providers should assess patients with acute respiratory illness for epidemiologic risk factors for avian influenza; If avian influenza is suspected, test for influenza via PCR, and subtype all influenza A-positive specimens.

Actions Requested

IDENTIFY

• Identify patients with acute respiratory illness (ARI)
• Assess ALL patients with ARI for epidemiologic risk factors for avian influenza inthe 10 days before symptom onset:
  • Close contact with sick or dead animals or their environments, especially birds, wildlife, livestock (including poultry), or domestic animals suspected of HPAI, OR
  • Consumption or handling of raw animal products or parts from potentially infected animals, OR
  • Close contact (within six feet) with a person who is suspected or confirmed to have avian influenza.
• Screen all patients with ARI (at minimum for Emergency Departments and inpatient settings) with the above questions; isolate patient and notify Local Health Jurisdiction if any response is “yes.”

ISOLATE

• Isolate patients with suspected or confirmed avian influenza in ALL healthcare settings.

INFORM

• At suspicion of avian influenza, IMMEDIATELY contact the Local Health Jurisdiction or Tribal Health Jurisdiction.

TEST

• Test ALL patients with ARI AND epidemiologic risk factors for avian influenza.
• Collect specimens from suspected avian influenza patients within 24 hours of presentation to the healthcare facility, and ideally within 7 days of symptom onset.
• Collect standard respiratory samples used for clinical decision making, AND the following additional specimens for HPAI testing (after notification to the LHJ):
  • A nasopharyngeal swab, AND;
  • A conjunctival swab in patients with conjunctivitis (with or without respiratory symptoms)
  • In patients with severe respiratory disease, lower respiratory tract specimens (e.g., endotracheal aspirate or bronchoalveolar lavage)
• Repeat testing using PCR for patients who previously tested negative for influenza A:
  • A negative influenza A PCR does not rule out avian influenza in patients with ARI and epidemiological risk factors; avian influenza should remain on the differential diagnosis.
  • Outpatient settings: Repeat influenza testing for patients who return with increased severity of symptoms.
  • Inpatient settings: Repeat influenza testing for at least two consecutive days unless an alternative diagnosis (e.g., COVID) is confirmed.
• Testing/subtyping is available at the WA DOH Public Health Laboratories (PHL).
  • Avian influenza testing is available at PHL with prior arrangement from the LHJ.
  • Specimens for influenza subtyping can be sent directly to PHL (no prior arrangement with LHJ needed) for the following specimen types:
    • All influenza A specimens that result as “unsubtypeable”
    • Specimens from hospitalized patients with risk factors for avian influenza, when subtyping is not available.
  • Follow PHL influenza specimen submission guidelines (PDF).

SUBTYPE

• Obtain subtyping for:
  • All influenza A-positive specimens from patients with epidemiologic risk factors for avian influenza.
  • Note: Unlike recommendations from previous years, subtyping is NOT required for hospitalized patients that do not have epidemiologic risk factors for avian influenza.
• Options for subtyping:
  • Option 1: Subtyping at hospital’s clinical lab or a commercial lab:
    • Subtyping result = H1 or H3: No further subtyping is necessary.
    • Subtyping result = H5 or “unsubtypeable”: Submit specimen to PHL.
  • Option 2: Subtyping request sent to PHL:
    • Facilities who do not have subtyping capability should submit specimens to PHL after communication with the LHJ.
  • Note for facilities using Laboratory Developed Tests (LDTs) for subtyping:
    • The LDT protocol should subtype for seasonal A(H1) and A(H3) viruses before, or in parallel with, A(H5) testing.
    • LDTs for influenza subtyping are NOT considered confirmatory; specimens must be sent to PHL for confirmatory subtyping.
• Note: Hospitals and labs participating in voluntary influenza subtyping surveillance (sentinel influenza surveillance network and RESP-NET) should follow established agreements/protocols.

TREAT

• Treat suspected avian influenza patients immediately with oseltamivir, do not wait for influenza confirmation.
• For hospitalized patients consider combination antiviral treatment (e.g., oseltamivir and baloxavir); refer to CDC’s Interim Guidance on the Use of Antiviral Medications.

ADVISE

• Advise patients not to handle sick or dead birds or other wildlife. Instead:  
  • Report sick or dead wild birds or other wild animals to the Washington State Department of Fish & Wildlife.  
  • Report sick or dead domestic animals, including backyard flocks or livestock with suspect avian influenza to the Washington State Department of Agriculture.
• WA DOH recommends seasonal influenza vaccine for patients 6 months of age and older.
  • While the seasonal influenza vaccine may not protect against avian influenza, it may prevent patients from coinfection.

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Resources        

• WA DOH: Avian Influenza
• WA DOH: Influenza Surveillance Data (Weekly Influenza Update)
• WA DOH: Influenza Virus Testing at the Washington Public Health Laboratories (PDF)
• Washington State Department of Agriculture: Avian Influenza in Livestock and Pets
• Washington State Department of Fish & Wildlife: Avian Influenza in Wild Animals
• CDC: Signs and Symptoms of Bird Flu in People
• CDC: Interim Guidance for Infection Control Within Healthcare Settings When Caring for Confirmed Cases, Probable Cases, and Cases Under Investigation for Infection with Novel Influenza A Viruses Associated with Severe Disease
• CDC: Interim Guidance on the Use of Antiviral Medications for Treatment of Human Infections with Novel Influenza A Viruses Associated with Severe Human Disease
• CDC: Clinician Brief: Evaluating and Managing Patients Exposed to Animals or Persons Infected with Novel Influenza A Viruses of Public Health Concern
• CDC and APHL: US 2026-2027 Influenza Season Surveillance Guidance (PDF)

Contact Us

Contact Whatcom County Health and Community Services at 360-778-6100

• 360-778-6100 Main Call Line – available M-F 8:30am to 4:30pm.
  • Afterhours Answering Service – available after 4:30pm and weekends, call 360-778-6100 and press 2 to be connected to the on-call manager or health officer.
• 360-778-6150 Communicable Disease Report Line – 24 hours a day 7 days a week
• 360-778-6103 Confidential Communicable Disease Fax – 24 hours a day 7 days a week
• 509 Girard Street, Bellingham WA 98225