Provider Alert: Updated Guidance for Influenza Testing and Subtyping

Situation Summary

Emergency Department visits for influenza are currently rising in Washington, indicating an early start to the 2026-2027 influenza season. 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. 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.

Report suspected cases of avian influenza, to using the contact information below.

Actions Requested

IDENTIFY

• Identify patients with acute respiratory illness (ARI) or other symptoms consistent with influenza. Symptoms of avian influenza can range from mild to severe.
• 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 (e.g., raw cow milk, products made with raw cow milk, and raw meat-based pet food), 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 if any response is “yes.”

ISOLATE

• Isolate patients with suspected or confirmed avian influenza in ALL healthcare settings:
  • Use contact, droplet, and airborne precautions with eye protection (goggles or face shield).
  • Use an airborne infection isolation room (a.k.a. negative pressure room) if available.
  • Maintain contact, droplet, and airborne precautions for the duration of illness or until consultation with public health has ruled out avian influenza.
  • If the patient is intubated, ensure a closed system and HEPA filter.

INFORM AND REPORT

• If you suspect avian influenza, IMMEDIATELY contact . The following are IMMEDIATELY notifiable:
  • All suspected and confirmed cases of novel influenza, including avian influenza (influenza A H5 or others); a negative influenza PCR does not rule out avian influenza.
  • All influenza A specimens that result as “unsubtypeable” (Influenza A positive test but specimen subtype not identifiable).

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/OR;
  • A nasal swab combined with an oropharyngeal swab (e.g., two swabs combined into one viral transport media vial). A single nasal or oropharyngeal swab is acceptable.
  • 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.
• 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.

Background

Avian influenza is a disease caused by influenza type A viruses, which naturally occur in wild aquatic birds worldwide. On rare occasions, avian influenza can infect people and make them sick. The risk of avian influenza increases during bird migration with possible spread to animals including commercial poultry, dairy farms, and backyard flocks.

CDC considers the risk of avian influenza infections to be low for the general public; WA DOH and CDC are closely monitoring the situation. As seasonal influenza activity increases in Washington and across the United States, the greatest risk to the general public is seasonal influenza. The best protection remains seasonal influenza vaccination. WA DOH publishes a Weekly Influenza Update for seasonal influenza.

Resources        

• Avian Influenza, DOH.
• Influenza Surveillance Data (Weekly Influenza Update), DOH.
• Influenza Virus Testing at the Washington Public Health Laboratories, DOH.
• Avian Influenza in Livestock and Pets, Washington Department of Agriculture.
• Avian Influenza in Wild Animals, Washington State Department of Fish & Wildlife.
• 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.
• US 2026-2027 Influenza Season Surveillance Guidance (PDF), CDC and APHL.

Contact and Reporting

Questions?

• For urgent issues, call (253) 649-1412.
• For non-urgent issues, call (253) 649-1413 and leave a message.
  • Includes reporting notifiable conditions 24 hours a day, 7 days a week.
  • Leave the patient’s name, date of birth and disease.