Brief Description

Presumptive identification of Influenza A/H5N1 (Asian lineage) and Influenza A (H7N9)

Laboratory Unit



Real-Time RT-Polymerase Chain Reaction

Specimen Collection

Avian Flu Information

CDC Interim Guidance on Specimen Collection & Testing for Avian Influenza

Avian Influenza Testing for suspect cases of highly pathogenic avian influenza (H5N1) or influenza A (H7N9) is available from the MSPHL only if indicated after a case investigation has been initiated. Refer to the Department of Health and Senior Service's (DHSS) Pandemic Influenza website, for instructions and to report any suspect case of avian influenza to DHSS. Note: primary point of contact is the Bureau of Communicable Disease Control and Prevention (573-751-6113 or 800-392-0272).

Consultation with the Bureau of Communicable Disease Control and Prevention (573-751-6113 or 800-392-0272) is required prior to collecting clinical specimens.


Kits for the submission of avian influenza A (H5N1) and avian influenza A (H7N9) specimens are certified for the transportation of infectious substances. These kits will be provided only after consultation with the Healthcare Associated Infections Coordinator.

Acceptable Specimen Type(s)

Nasopharyngeal Swab
Nasopharyngeal Swab / Oropharyngeal Swab combination

Nasal Aspirate or Wash Endotrachial Aspirate 
Bronchoalveolar Lavage

Autopsy specimens that are acceptable: Fresh-frozen, unfixed lung tissue

See Avian Flu Information link above for further information on additional autopsy and blood specimens that can be sent to CDC for testing.

If possible, in order to increase the potential for H7N9 or H5N1 virus detection, multiple respiratory specimens from different sites should be obtained from the same patient on at least two consecutive days.

Test Request Form(s)

Possible Results

Presumptive Positive for Influenza A/H5, specimen being referred to CDC for additional testing
Influenza A H7N9 Detected
Influenza Not Detected
Unsatisfactory for Testing

Unacceptable Conditions

Received warm
Improperly identified
Specimen not identified
Specimen not in viral transport medium
Not approved by Healthcare Associated Infections Coordinator
Specimen collected with improper collection device
Specimen not an acceptable type

Interfering Substances

Use only viral transport medium and synthetic Dacron/flocked swab or equivalent.  Do not use wooden shaft or cotton swab. 

Result Reported

Directly to submitting agency upon completion of testing.


None. Testing performed only after consultation.

CPT Codes




Additional Information

Because the sensitivity of commercially available rapid diagnostic tests for influenza may not always be optimal, RT-PCR testing may be performed even if influenza rapid diagnostic testing is negative on patients meeting the clinical criteria for avian influenza infection.

Highly pathogenic avian influenza A (H5N1) is classified as a select agent and must be worked with under stringent Biosafety Level (BSL) 3+ laboratory conditions. Therefore, respiratory virus cultures should not be performed in most clinical laboratories and such cultures should not be ordered for patients suspected of having H5N1 infection.

Requests for Virus Isolation collection kits (these kits should be requested for all novel strains of influenza including highly pathogenic avian influenza) should be directed to the SPHL at 573-751-3334. Instructions for specimen collection and transport may be found in the MO SPHL Avian Influenza Laboratory Information instruction sheet (below).

Refer to the CDC infection control precautions when collecting and handling laboratory specimens.

Avian Flu Information

Avian Influenza (H5N1) Lab Fact Sheet

Laboratory Guidelines For Influenza Testing With The Presence Of Avian Influenza A H5N1

Pandemic Influenza
Agricultural Select Agent Program

CDC – Avian Flu