Hygienic Laboratory Influenza Surveillance Testing2019-2020 Testing Guidance
For the 2019-2020 season, SHL and the Iowa Department of Public Health request the following specimens to be submitted for molecular testing at SHL.
- Outpatient facilities - Submit up to 2 specimens per week to contribute to surveillance regardless of in-house test method.
- Inpatient - hospitalized patients with suspected Influenza and without other apparent cause regardless of in-house method or tests results.
- Patients from a defined population (e.g., schools, long-term care facilities) when an outbreak is suspected
- Patients where confirmation is desired because of special circumstances. (Please note these circumstances on the test request form when submitting to the Hygienic Lab).
- ILINet Sentinel Providers are asked to submit specimens on patients with influenza-like illness per IDPH guidelines.
I. Influenza Specimen Collection, Submission and Results
Please submit the patient’s specimen to SHL for testing by real-time PCR (RT-PCR) if it meets the criteria as described in the algorithm. RT-PCR is a molecular method of virus detection that is more sensitive and specific than point of care rapid tests.Specimen Collection
Patients with influenza-like illness (optimally within three days of symptom onset):
- Combined nasal swab plus throat swab (two swabs in one tube transport medium)
- Nasopharyngeal swab (flocked swab preferred)
- Do not submit swabs or specimens that have been used for rapid testing
- Must be in viral transport medium (OK to use any type of viral transport media, but not bacterial transport media)
Patients hospitalized with pneumonia or other secondary infections when more than seven days have elapsed from the onset of influenza-like illness:
- Lower respiratory specimens such as sputum or BAL
The following specimens should be considered for patients who are intubated or undergoing bronchoscopy:
- Endotracheal aspirate
- Bronchoalveolar lavage (BAL)
If a patient with pneumonia or other secondary infection is not intubated or undergoing bronchoscopy, then a combined nasal swab plus throat swab (two swabs in one tube transport medium) or nasopharyngeal swab should be obtained.
Test Request Form
- Use the SHL test request form generator, select the Viral and Bacterial PCR form, select your organization from the pick list below, and click submit to generate your customized test request form.
II. Transportation of specimens to SHL
- The CDS courier can be used to transport specimens to SHL. Please contact Ron Hardy (CDS) at 515/289-9990 or Becky Teske (SHL) at 319/335-4500 to arrange courier service. If your facility does not routinely use the CDS courier, bring the specimen to the nearest lab that does have courier pick up -- usually the closest hospital laboratory.
- Please note this is a different request than the SHL Newborn Screening (NBS) courier pick up. Please make certain you do not use the NBS envelope (or choose NBS envelope on the CDS website) because these envelopes go to the laboratory in Ankeny and influenza testing is performed in Coralville.
- Other transport options include the USPS, commercial carriers, or other courier services.
III. Accessing Your Results
- Results are available via the OpenELIS Web Portal. If your facility does not have access to your results via a web portal account, contact SHL to obtain permission and training. Call 319/335-4358, email email@example.com, or download the SHL web portal application on the “Test Results” page and submit the completed form to SHL.
- Facilities without web portal access will receive results via USPS.
IV. Result Interpretation
All testing is performed using the CDC Human Influenza Virus Real–Time RT–PCR Diagnostic Panel and the results are reported as follows:
Test: Influenza A (this tests for subtypes of influenza A virus including Seasonal H1, 2009 pandemic H1N1 and Seasonal H3).
Interpretation: This Real Time-PCR test detects Influenza A virus. It will detect ALL types of Influenza A. When Influenza A is not detected, no further testing is necessary. If Influenza A virus is detected, the virus will be subtyped to distinguish it as seasonal H3 or 2009 pandemic H1N1.
Test: Influenza A subtype
Interpretation: This Real-Time PCR test detects Influenza A virus. It will detect both seasonal H3 or 2009 pandemic H1N1.
Test: Influenza B
Interpretation: This Real-Time PCR test detects Influenza B virus. It will detect both Yamagata and Victoria lineage.
Test: Influenza B subtyping
Interpretation: This Real-Time PCR test will distinguish between Yamagata and Victoria lineage Influenza B viruses. It is reported as EITHER Yamagata or Victoria.
- NOTE: If a specimen is positive for more than one subtype, it is most likely due to collection of the specimen within a few days of the patient receiving the live virus vaccine. Co-infections do occur, but are rare.
If a specimen is positive for Influenza A but negative for all subtypes, it is considered inconclusive. This is most likely due to a weakly positive sample that does not contain sufficient amounts of virus for subtyping, but could also reflect an infection with a novel strain of influenza virus. Any of these unusual results are investigated by SHL.
Influenza surveillance serves the following purposes:
- Demonstrates when and where influenza viruses are circulating in Iowa.
- Identifies the strains of influenza circulating in communities for treatment considerations.
- Allows for characterization of new or antigenic variant viruses, match to current vaccine and determination of viruses to include in next season's vaccine.
Last updated Sept. 19, 2019.