Interim Guidance for Enhanced Influenza Surveillance: Additional Specimen Collection for Detection of Influenza A (H3N2) Variant Virus Infections


This document is an update to interim enhanced surveillance guidance posted in 2012. In anticipation of the 2014 agricultural fair season, states should consider expanding surveillance to include reverse-transcription polymerase chain reaction (RT-PCR) testing of specimens from ILINet providers statewide, of specimens collected from people with ILI reporting recent swine contact or agricultural fair attendance, and of specimens collected from people with unusual or severe presentations of ILI. States should also consider collection of specimens from outbreaks of ILI among children in child-care and school settings, since these settings have been associated with person-to-person H3N2v virus transmission in 2011. CDC will continue to evaluate new information as it becomes available and will update this guidance as needed.


Since August 2011, a number of human infections with a variant influenza A H3N2 virus (“H3N2v”) have been detected in the United States (see Case Count: Detected U.S. Human Infections with H3N2v by State since August 2011). Influenza viruses that typically infect swine are referred to as “variant” when they infect humans. During these outbreaks, most cases reported agricultural fair attendance and contact with swine prior to illness. Few instances of person-to-person transmission were identified, and there was no evidence of sustained community-wide transmission. Confirmed H3N2v cases were identified primarily among children (<18 years of age), and limited serologic studies indicate that children, primarily those born after 2001 (age ≤9 years at 2010), have increased susceptibility to H3N2v. However, some adult H3N2v cases were identified.

This document provides interim guidance to state and local health departments for enhanced surveillance and testing by (RT-PCR) for influenza viruses. Use of RT-PCR testing is important in order to identify which influenza A virus subtypes (e.g. H3N2v viruses versus seasonal H1N1 or H3N2 viruses) are circulating. These guidelines have been developed in an effort to facilitate timely detection and investigation of H3N2v cases by targeting patients with influenza-like illness (ILI) for influenza testing by RT-PCR.

CDC would like state and local health departments to consider the following recommendations for influenza surveillance and testing.

  1. All state public health laboratories should use the CDC Human Influenza Real-Time rRT-PCR FLU Diagnostic Panel to screen specimens for InfA, InfB, and RP.
  2. Test all InfA-positive specimens with the CDC Influenza A Subtyping kit using all primer/probe sets: H1, H3, pdmInfA and pdmH1. Detailed guidance for testing can be found in the influenza surveillance diagnostic testing algorithm disseminated recently by Association of Public Health Laboratories [27 KB, 1 page]. Specimens that are positive for H3N2v virus should be sent to CDC Influenza Division for additional testing as soon as possible.
  3. Conduct contact tracing of confirmed influenza A (H3N2)v cases to gather more information about the epidemiology of the virus and modes of transmission. Contact tracing is essential to evaluate potential person-to-person transmission.
  4. When seasonal influenza viruses circulate at low levels, CDC recommends collecting specimens from patients with ILI, and sending these specimens to the state or local laboratory for rRT-PCR testing. States should specifically consider collection of specimens across the state from patients presenting with ILI in the following high priority areas:
    1. All ILINet providers statewide.
    2. Medically attended ILI and acute respiratory infection (ARI) in patients who have had recent contact (< 7 days prior to illness onset) with swine or recent attendance at an agricultural event where swine are present.
    3. ILI outbreaks statewide, particularly among children in child care and school settings, since these settings were associated with person-to-person transmission of H3N2v in the past.
    4. Unusual or severe presentations of ILI statewide, including hospitalized persons.
    5. Medically attended ILI and acute respiratory infection (ARI) in children in areas where confirmed H3N2v cases have occurred.

CDC will continue to evaluate new information as it becomes available and will update this guidance as needed.