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Interim Guidance for Specimen Collection, Processing, and Testing for Patients Who May Be Infected with Avian Influenza A (H7N9) Virus


As of June 3, 2013, health officials have reported more than 130 cases of human infection with a new avian influenza A (H7N9) virus from 10 different provinces and municipalities in mainland China and Taiwan. Most patients were hospitalized with severe respiratory illness and reported poultry contact prior to illness onset. Although clusters of human cases of H7N9 have been reported, there has been no evidence of sustained human-to-human transmission of this virus. Poultry also have tested positive for avian influenza A (H7N9) virus in parts of China that generally overlap with the provinces where human cases have been detected. Avian influenza A (H7N9) virus has not been detected in humans or animals outside China, and no cases of human infection with avian influenza A (H7N9) have been identified in the United States.


This document provides interim guidance for clinicians and public health professionals on appropriate specimen collection, storage, processing, and testing for patients who may be infected with avian influenza A (H7N9) virus in the United States. Current influenza A (H7N9) case definitions and recommendations for patient testing should also be consulted.

When Specimens Should Be Collected

The duration of shedding of avian influenza A (H7N9) virus in humans is unknown, and there are currently no data describing prolonged shedding of infected individuals with this virus. Therefore, until data are available, the estimated duration of viral shedding is based upon seasonal influenza virus infection. Specimens should be obtained for avian influenza A (H7N9) virus testing as soon as possible after illness onset, ideally within 7 days of illness onset. However, as some persons who are infected with seasonal influenza viruses are known to shed virus for longer periods (e.g., children and immunocompromised persons), specimens should be tested for avian influenza A (H7N9) virus even if obtained after 7 days from illness onset.

Preferred Respiratory Specimens

The following should be collected as soon as possible after illness onset: (i) a nasopharyngeal swab, or (ii) a nasal aspirate or wash, or (iii) two swabs combined into one viral transport media vial (e.g., combined nasal swab with oropharyngeal swab or combined nasopharyngeal swab with oropharyngeal swab). If these specimens cannot be collected, a single nasal swab or single oropharyngeal swab is acceptable. For patients with lower respiratory tract illness, a lower respiratory tract specimen (e.g., an endotracheal aspirate or bronchoalveolar lavage) is preferred. 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.


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 sent to state public health laboratories should be shipped in the appropriate packaging and according to instructions by the laboratory. 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.

Specimens to be tested for avian influenza A (H7N9) virus that are shipped from state public health laboratories to CDC should include all information required for seasonal influenza surveillance isolate or specimen submission. Before sending specimens, state and local health departments should contact the CDC Influenza Division Epidemiology and Prevention Branch at (404) 639-3747 (Monday – Friday, 8:30 AM - 5:00 PM or the on-call epidemiologist at (770) 488-7100 (all other times).

Ship specimens to CDC at the following address:

Virology, Surveillance and Diagnosis Branch
ATTN: Steve Lindstrom
Influenza Division, NCIRD
Centers for Disease Control and Prevention
1600 Clifton Road NE MS G-16
Atlanta, GA 30333

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. 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 CDC and their state or local public health laboratory for additional testing (see below).

Rapid influenza diagnostic tests (RIDTs) and immunofluorescence tests also have unknown sensitivity and specificity to detect human infection with avian influenza A (H7N9) virus in clinical specimens. These tests may give a positive influenza A result for a specimen containing avian influenza A (H7N9) virus. However, negative results from either type of test do not exclude influenza virus infection, especially in patients with signs and symptoms suggestive of influenza. Therefore, a negative test result could be a false negative and should not be used as a final diagnostic test for influenza, including avian influenza A (H7N9) virus infection.

Testing at State Health Departments

Specimens to be tested for avian influenza A (H7N9) virus should be sent first to public health laboratories. Testing can be performed by public health laboratories on a portion of the specimen, while a portion of the sample should be set aside in case there is a need to ship it to CDC.  All state public health laboratories should use the CDC Human Influenza Real-Time RT-PCR Diagnostic Panel to screen specimens for InfA, InfB, and RP.

Health departments should test all InfA-positive specimens with the CDC Influenza A Subtyping kit using all primer/probe sets: H1, H3, pdmInfA, and pdmH1. Avian influenza A (H7N9) viruses will be positive for the influenza A target, but negative for the seasonal influenza A (H3) target, negative for the seasonal influenza A (H1) target, negative for the pandemic 2009 (pdmH1) target, and negative for the nucleoprotein (NP) gene target (pdmInfA) using the CDC Human Influenza Real-Time RT-PCR Diagnostic Panel. Public Health officials should contact CDC immediately if they obtain unsubtypable results when testing an influenza specimen.

Testing with the CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel-Influenza A/H7 (Eurasian Lineage) Assay should not be performed unless the patient meets the currently recommended clinical and epidemiologic criteria for testing. The CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel-Influenza A/H7 (Eurasian Lineage) Assay can be performed for the presumptive identification of virus in patients who may be infected with influenza A/H7(Eurasian Lineage) (this includes the avian influenza A (H7N9) virus first identified in China in 2013). Specimens that are unsubtypable or that are presumptive positive for influenza A/H7 should be sent to CDC, Influenza Division, Virus Surveillance and Diagnostic Branch Laboratory for confirmatory testing. Laboratories should not attempt diagnosis of patients who may be infected with avian influenza A (H7N9) virus using viral culture.

Antiviral treatment should not be withheld or delayed pending collection of specimens or laboratory testing. Empiric treatment with a neuraminidase inhibitor antiviral drug (oral oseltamivir or inhaled zanamivir) should be administered immediately according to current guidelines. For more information, see CDC’s interim guidance on the use of antiviral agents for treatment of human infections with avian influenza A (H7N9).

CDC will continue to evaluate new information as it becomes available and will update this guidance as needed. For further assistance with these recommendations, please contact CDC at (770) 488-7100.


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