Specimen Collection and Testing for Seasonal Influenza - Minnesota Dept. of Health

Specimen Collection and Testing for Seasonal Influenza

On this page:
When to send specimen
Appropriate specimen types
Specimen collection
Specimen submission forms
Shipping to MDH-PHL
Additional influenza surveillance programs
Reporting influenza
Other influenza information

When to send specimen

Send a specimen to the MDH Public Health Laboratory (MDH-PHL) in the following circumstances:

  • Hospitalized surveillance – specimens submitted from persons who are hospitalized with influenza-like illness* (ILI) or clinical suspicion of influenza or deceased following ILI* or clinical suspicion of influenza.
    • It is important to send a specimen on any hospitalized patient with ILI* or clinical suspicion of influenza; even if rapid influenza testing is negative or if testing was not performed.
    • If your laboratory is performing onsite influenza testing by PCR, positive influenza A specimens that are subtyped as H1N1pdm or H3 do not need to be routinely submitted.
      • Positive influenza A specimens that are unsubtyped, subtyped as "seasonal H1," or "indeterminate" do need to be submitted to MDH-PHL for further characterization as they could be variant influenza strains.
      • All positive influenza B specimens should be submitted to MDH-PHL.
      • Specimens that are negative by PCR for influenza A and B do not need to be submitted to MDH-PHL.
    • Specimens from deceased patients following confirmed or suspect influenza illness should be submitted for all patients.
  • Cluster investigation or other unusual circumstance for which MDH epidemiology has requested a specimen(s) be sent to MDH-PHL.
  • Sentinel surveillance – these facilities are pre-determined.
  • Laboratory surveillance - isolates from virology laboratories only.

Appropriate specimen types

For patients admitted with ILI* or clinical suspicion of influenza without evidence of pneumonia or other lower respiratory disease, submit one upper respiratory specimen per patient.

Preferred specimen:

  • Nasopharyngeal swab

Other acceptable specimens:

  • Nasal swab
  • Nasal wash/aspirate
  • Throat swab
  • Combined nasal swab with an oropharyngeal swab
  • Viral culture

For patients admitted with ILI* or clinical suspicion of influenza who also have evidence of pneumonia or other lower respiratory disease, submit one upper respiratory specimen and one lower respiratory specimen (do not perform a procedure such as bronchoscopy solely for the purpose of collecting a specimen for testing by MDH-PHL) per patient.

Submit an upper respiratory specimen in addition to one or more of the following:

  • Bronchial alveolar lavage (BAL)
  • Tracheal aspirate (if intubated)
  • Bronchial wash

* Influenza-like illness (ILI) is defined as fever (measured or subjective) and cough and/or sore throat in the absence of a known disease other than influenza.

Specimen collection

  • Place respiratory specimens into viral transport medium for transport to MDH-PHL. Washes and aspirates may be collected in saline and placed into 1-3 milliliters viral transport media.
  • Store at refrigeration temperature until transport.
  • Freeze specimen if it will not reach MDH-PHL within 7 days.

Specimen submission forms

Submission forms and guidance documents are available at Forms for the Infectious Disease Laboratory.

Shipping to MDH-PHL

  • Ship specimens to MDH-PHL by an overnight delivery service.
    • For refrigerated specimens, use cold packs to keep specimens at 4 degrees C. Put in a container that will maintain refrigeration temperature throughout transport.
    • For frozen specimens, use dry ice to keep specimens frozen. Put in a container that will maintain frozen temperature throughout transport.
    • Note: It is the responsibility of the submitting laboratory to determine the appropriate packaging and shipping for patient specimens and culture isolates. See the U.S. Department of Transportation's guidance on Transporting Infectious Substances Safely for more information.
  • Ship to:
  • Minnesota Department of Health
    Public Health Laboratory
    Attn: Biological Accessioning
    601 Robert St. N
    St. Paul, Minnesota 55155-2531

Additional influenza surveillance programs

MLS Laboratory Influenza Surveillance Program
MDH Weekly Influenza Activity - Statistics
The MN Lab System (MLS) Laboratory Influenza Surveillance Program is made up of more than 100 clinic- and hospital-based laboratories, voluntarily submitting testing data on a weekly basis. These laboratories perform rapid antigen testing (DFA, rapid EIA) for influenza and respiratory syncytial virus (RSV), as well as rapid molecular testing for influenza. Increasingly, more laboratories are performing molecular testing for influenza and RSV, while significantly fewer labs perform confirmatory culture testing for influenza and RSV.

Tracking the laboratory results assists health care providers with patient diagnosis of influenza-like illness and provides an indicator as to the progression of the influenza season as well as prevalence of disease in the community.

If your laboratory is interested in participating in this program, please call: 651-201-5035.

MLS Virology Laboratory Isolate Surveillance
Viral isolates are subtyped to monitor for the introduction of new influenza virus strains for comparison to the current vaccine subtypes. MDH-PHL performs hemagglutinin subtyping on isolates submitted from virology laboratories serving MN patients. Selected influenza isolates are forwarded to CDC for neuraminidase subtyping.

U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet)
Physicians and health care providers across the state help to monitor influenza throughout the flu season. ILINet providers fill out a weekly report detailing the number of patients they've seen with influenza-like illness. They also submit additional influenza specimens to the MDH-PHL according to the ILINet program guidelines.

Novel Influenza A Surveillance
Call MDH at 651-201-5414 or 1-877-676-5414
if you have a suspect novel influenza A. Do not attempt to perform viral culture. Culture for novel influenza should only be done at a BSL3+ or BSL4 facility.

Reporting influenza

Reporting Influenza - information on what to report, how to report, and who is required to report.


  • For an MDH epidemiologist, call 651-201-5414 or 1-877-676-5414.
  • During business hours you can call the Virology Supervisor at 651-201-5035.
Updated Friday, 02-Apr-2021 09:59:14 CDT