Hygienic Laboratory Influenza Surveillance Testing
For the 2015-2016 season, SHL and the Iowa Department of Public Health requests the following specimens to be submitted for molecular testing at SHL:
- Laboratories that perform rapid tests should submit positive specimens to SHL for confirmation until one specimen is confirmed because point of care “rapid” tests have a poor Positive Predictive Value during times of low prevalence. Confirmation via molecular testing can help to interpret rapid test performance and indicate when results are more reliable.
- Hospitalized in-patients with influenza-like illness without other apparent cause;
- 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 circumstances on the test request form when submitting to the Hygienic Lab).
- ILINet Sentinel Providers: 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 3 days of symptom onset):
- Nasopharyngeal swab (flocked swab preferred)
- Nasal swab plus throat swab (2 swabs in one tube transport medium)
- Lower respiratory specimens such as sputum or BAL
- Endotracheal aspirate
- Bronchoalveolar lavage (BAL)
If a patient with pneumonia or other secondary infections is not intubated or undergoing bronchoscopy, then a nasopharyngeal swab or combined nasal swab plus throat swab (2 swabs in one tube transport medium) should be obtained.
Test Request Form
- Fill out the SHL test request form generator and select Viral and Bacterial PCR and DFA.
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 web-based result reporting system. If your facility does not have access to your results via the web page, then contact SHL to obtain permission and training. Call 319-335-4358, email email@example.com, or download the Results Web Access application on the “Test Results” screen and submit the completed form to SHL.
- Facilities without web 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 including seasonal influenza A H1, seasonal H3, 2009 pandemic A/H1N1 “swine-like” strain and classic swine viruses. 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 H1, seasonal H3 or 2009 pandemic H1N1.
Test: Influenza A subtype H1 (seasonal H1)
Interpretation: This Influenza A real-time RT-PCR test detects the seasonal influenza H1 strain and will NOT detect the 2009 pandemic H1N1 strain type.
Test: Influenza A H1N1 swine-like
Interpretation: This real-time RT-PCR test detects the Influenza 2009 pandemic H1N1 strain.
Test: Influenza A subtype H3 (seasonal H3)
Interpretation: This real-time RT-PCR test detects the seasonal influenza A/H3 strain type and will NOT detect the 2009 pandemic H1N1 strain type.
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. 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. 18, 2015.