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Content on this page was developed during the 2009-2010 H1N1 pandemic and has not been updated.

  • The H1N1 virus that caused that pandemic is now a regular human flu virus and continues to circulate seasonally worldwide.
  • The English language content on this website is being archived for historic and reference purposes only.
  • For current, updated information on seasonal flu, including information about H1N1, see the CDC Seasonal Flu website.

Interim Guidance for Influenza Surveillance: Prioritizing RT-PCR Testing in Laboratories

October 9, 2009 11:00 AM ET

This document provides interim guidance for state and local health departments, hospitals, and clinicians participating in surveillance activities regarding which patients to prioritize for testing by RT-PCR for influenza surveillance. Based on the continuing spread of 2009 H1N1 virus since the spring and continuing into the fall and increased demand for influenza testing, these guidelines have been developed in an effort to prioritize patients for testing by RT-PCR for influenza for surveillance purposes.

The recommendations in this interim guidance are made to support surveillance activities for influenza; they do not address prioritization of testing for other purposes. Confirmation of 2009 influenza H1N1 virus infection may also be important for clinicians taking care of patients. Guidance on prioritization of diagnostic testing for clinical care purposes can be found at Interim Recommendations for Clinical Use of Influenza Diagnostic Tests During the 2009-10 Influenza Season.

Use of real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) testing is important for surveillance in order to identify which influenza A subtypes (e.g. 2009 H1N1 versus seasonal H1N1 or H3N2 viruses) are circulating. For surveillance purposes, CDC recommends that the following patients be prioritized for rRT-PCR testing:

  • Patients presenting to healthcare providers participating in the US Outpatient Influenza-like Illness Surveillance Network (ILINet) who meet the surveillance case definition of influenza-like illness (ILI*).
  • Hospitalized patients for whom influenza infection is clinically suspected despite a negative result on a rapid influenza diagnostic test.
  • Patients whose deaths are believed to be influenza-associated.

*ILI is defined as fever (temperature of 100°F [37.8°C] or greater) and a cough and/or a sore throat in the absence of a KNOWN cause other than influenza.

Specimen Collection and Storage

For information on specimen collection and storage, please see Interim Recommendations for Clinical Use of Influenza Diagnostic Tests During the 2009-10 Influenza Season.

Once collected, clinicians should contact their state or local health department to facilitate transport and timely diagnosis at a state public health laboratory. State public health laboratories should perform testing to determine influenza type and subtype on all submitted samples that are positive for influenza.

RT-PCR Diagnostic Tests

State public health laboratories in the United States have been provided with reagents and procedures from CDC to perform the CDC rRT-PCR Flu Panel (in vitro diagnostic seasonal influenza typing and subtyping assay) and the CDC rRT-PCR Swine Flu Panel (pandemic 2009 A/H1 influenza subtyping assay) under Emergency Use Authorization. State and local health department guidelines will determine which specimens can be submitted to public health laboratories for rRT-PCR testing. Additional FDA-authorized rRT-PCR assays have been developed for detection and characterization of influenza that can detect 2009 H1N1 influenza. Information about those assays can be found at: Medical Devices and Flu Emergencies

Also see interim guidance available on the 2009 H1N1 Flu website including:

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