Interim Guidance on Specimen Collection, Processing, and Testing for Patients with Suspect Influenza A (H3N2)v Virus Infection

This document is intended for public health professionals to provide interim guidance on appropriate specimen collection, storage, processing, and testing for patients with suspected influenza A (H3N2) variant ([H3N2]v) virus infection. These guidelines for specimen collection, storage, processing, and shipping are consistent with guidance for the submission of seasonal influenza viruses to the laboratory.

Case Definitions

Review more information on definitions for confirmed, probable, and suspect cases at Interim Guidance on Case Definitions to be Used For Investigations of Influenza A (H3N2) Variant Virus Cases.

Duration of Viral Shedding

The duration of shedding of influenza A (H3N2)v virus is unknown. Therefore, until data are available, the estimated duration of viral shedding is based upon seasonal influenza virus infection. Infected persons should be assumed to be contagious up to 7 days from illness onset. Infected persons can shed virus and are potentially infectious from the day prior to illness onset until resolution of fever. Some persons who are infected might shed virus and be contagious for longer periods (e.g. young infants and immunocompromised persons).

Testing for Influenza A (H3N2)v Virus

Clinicians should consider testing suspected cases of influenza A (H3N2)v virus infection, especially those with severe illness, by obtaining an upper respiratory specimen.

Preferred Respiratory Specimens

The following should be collected as soon as possible after illness onset: nasopharyngeal swab, nasal aspirate or wash or a combined nasopharyngeal swab with oropharyngeal swab. If these specimens cannot be collected, a nasal swab or oropharyngeal swab is acceptable. For patients who are intubated, an endotracheal aspirate should also be collected. Bronchoalveolar lavage (BAL) and sputum specimens are also acceptable. Specimens should be placed into sterile viral transport media and immediately placed on refrigerant gel-packs or at 4°C (refrigerator) for transport to the laboratory. Recommended infection control guidance is available for persons collecting clinical specimens in clinics and other clinical settings at Prevention Strategies for Seasonal Influenza in Healthcare Settings.


Ideally, swab specimens should be collected using swabs with a synthetic tip (e.g., polyester or Dacron®) and an aluminum or plastic shaft. Swabs with cotton tips and wooden shafts are not recommended. Specimens collected with swabs made of calcium alginate are not acceptable. The swab specimen collection vials should contain 1-3ml of viral transport medium (e.g., containing, protein stabilizer, antibiotics to discourage bacterial and fungal growth, and buffer solution).

Storing Clinical Specimens

Respiratory specimens should be kept at 4°C for no longer than 3 days. Specimens can alternatively be frozen at ≤-70°C. Avoid freezing and thawing specimens if at all possible.

Shipping Clinical Specimens

Clinical specimens should be shipped to the laboratory in the appropriate packaging. If clinical specimens will be examined within 72 hours after collection, keep the specimen at 4°C (2-8 °C) and ship on refrigerant gel-packs, otherwise store frozen at ≤-70°C and ship on dry ice. Avoid freezing and thawing specimens. Viability of some pathogens from specimens that were frozen and then thawed is greatly diminished.

All specimens should be labeled clearly and include information requested by your state public health laboratory. Suspected influenza A (H3N2)v specimens shipped from the state public health laboratory to CDC should include all information required for seasonal influenza surveillance isolate or specimen submission.

Diagnostic Testing

The performance of current Food and Drug Administration (FDA) cleared diagnostic tests for influenza has been demonstrated for seasonal human influenza viruses as described by the manufacturer package insert. Performance has not been demonstrated with novel influenza A viruses; these viruses only infect humans sporadically. However, some diagnostic assays may detect the presence of novel influenza A viruses.

Molecular assays may detect novel influenza A viruses, but will not differentiate novel influenza A viruses from seasonal influenza A viruses. For these assays a novel influenza A virus:

  • May give an influenza A “unsubtypable” result. Clinicians and laboratorians using molecular assays that are capable of detecting all currently circulating influenza A subtypes who identify an “unsubtypable” result should contact their state or local public health laboratory for additional testing.
  • May give a false positive result for human influenza A(H3) viruses

Rapid influenza diagnostic tests (RIDTs) and immunofluorescence tests also have unknown sensitivity and specificity to detect human infection with influenza A (H3N2)v virus in clinical specimens. These tests may give a positive influenza A result for a specimen containing influenza A (H3N2)v virus. However, negative results from either type of test do not exclude influenza virus infection in patients with signs and symptoms suggestive of influenza. Therefore, a negative test result could be a false negative and should not be assumed a final diagnostic test for influenza A (H3N2)v virus infection.

Specimens from suspected influenza A (H3N2)v cases should be evaluated first by qualified public health laboratories prior to sending to CDC, if possible. Influenza A (H3N2)v viruses will be positive for the nucleoprotein (NP) gene target (pdmInfA) of the CDC Human Influenza Real-Time RT-PCR Diagnostic Panel as well as for the influenza A and seasonal influenza A (H3) targets. Qualified public health laboratories obtaining this result should contact the CDC, Influenza Division, Virus Surveillance and Diagnostic Branch Laboratory immediately. All suspected novel influenza A viruses and influenza A (H3N2)v specimens should be sent to CDC for confirmatory testing. Confirmation of influenza A (H3N2)v virus is performed only at CDC at this time.

Note: Antiviral treatment should not be withheld from patients with suspected influenza if the patient is hospitalized, has severe or progressive illness, or the patient has an underlying condition that places them at increased risk for influenza-related complications, even if they test negative for influenza.

For more information, see Antiviral Drugs.