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viral and rickettsial disease laboratory

Any Suspect or Laboratoy Confirmed Cases of Novel Influenza Should be Reported to the Local Health Department AND CDPH Immediately.

The CDPH Viral and Rickettsial Disease Laboratory (VRDL) Respiratory and Gastroenteric Diseases Section serves as a virologic reference laboratory offering diagnostic and specialized testing for influenza and many other viral respiratory pathogens and is one of three National Influenza Reference Centers in the United States. VRDL routinely performs diagnostic testing in a variety of situations, including institutional or community respiratory outbreaks, individual cases of severe respiratory illness, and outpatient cases of influenza-like illness submitted by Centers for Disease Control and Prevention (CDC) Influenza Sentinel Providers. The VRDL testing capabilities for influenza include cell culture for virus isolation, real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza typing and sub-typing, strain characterization and antiviral resistance testing. Most recently the VRDL has incorporated whole genome sequencing for influenza virus strain typing for situational awareness of circulating influenza viruses.

In the event of the emergence of a novel influenza A virus and potential epidemic/pandemic, the VRDL will work closely with the CDC and our local public health laboratory partners to provide molecular testing for influenza virus, including rRT-PCR testing, to identify and characterize the virus and offer confirmatory testing as needed. Antiviral resistance testing may be performed on a subset of specimens tested to monitor for emergence of drug resistance, as deemed necessary. Other testing may be provided, depending on circumstances as the situation develops.

Laboratory Testing for Novel Influenza A (including avian and swine influenza) from Human Specimens

Diagnostic testing is recommended for human cases of suspected novel influenza A (of swine or avian origin). Active infection with swine or avian influenza can only be confirmed by polymerase chain reaction (PCR) assays, including sub-typing and further characterization by other specialized assays. Molecular tests for influenza, such as rRT-PCR, are available at certain local public health laboratories in California and the CDPH Viral & Rickettsial Disease Laboratory (VRDL).  Confirmatory testing with PCR that is specific for novel influenza A subtypes is also available at VRDL and the CDC. After review by the local public health department, patient specimens should be submitted to VRDL through the local public health department or laboratory. Testing will be prioritized based on review of epidemiological information provided by the local health department. Questions regarding specimen submission for suspected cases of novel influenza A infection should be directed to the local health department.

Commercial rapid influenza antigen testing in the evaluation of suspected novel influenza cases should be interpreted with caution. The sensitivity and specificity of rapid antigen testing for identifying novel influenza is unknown. A negative result does not exclude a diagnosis of novel influenza A. A positive result may be helpful, but does not distinguish between seasonal and novel influenza viruses. Therefore, if a patient tests negative for influenza by rapid antigen testing, specimens should be sent for further characterization (including rRT-PCR for type and sub-type) to the local public health laboratory or the VRDL. More information on the utility of rapid antigen testing for influenza is available at the CDC's Rapid Diagnostic Testing for Influenza: Information for Clinical Laboratory Directors information page.

Diagnostic laboratory work on clinical samples from suspect novel influenza A (e.g., identified by rapid antigen testing or PCR) can be performed under BSL-2 conditions.  All sample manipulations should be performed inside an appropriate biological safety cabinet (BSC). Molecular testing for novel influenza A virus should be done at a local public health laboratory approved to perform this testing. Virus isolation procedures for novel influenza A virus from clinical specimens should NOT be attempted by hospital or private laboratories, or by local public health laboratories.


  • All waste disposal procedures should be followed as outlined by your facility's standard laboratory operating procedures

Appropriate Disinfectants

  • 70 % Ethanol

  • 5 % Lysol

  • 10 % bleach, made daily

Additional information on biosafety recommendations for influenza virus can be found at the CDC's Biosafety in Microbiological and Biomedical Laboratories Fifth edition (PDF).

Infection Control Precautions For Specimen Collection

For collecting respiratory specimens from an ill confirmed or suspected novel influenza case, the following is recommended:

  1. Infection control precautions during specimen collection should include the use of gloves, gown, goggles or face shield, and a fit-tested respirator with an N-95 or higher rating.  A loose-fitting powered air-purifying respirator (PAPR) may be used if fit-testing is not possible (for example, if the person has a beard).

  2. When completed, place all personal protective equipment in a biohazard bag for appropriate disposal.

  3. Wash hands thoroughly with soap and water or alcohol-based hand gel

More information on bio-safety recommendations can be found on the CDC's Interim Guidance for Infection Control Within Healthcare Settings When Caring for Confirmed Cases, Probable Cases, and Cases Under Investigation for Infection with Novel Influenza A Viruses Associated with Severe Disease information webpage.

Minimum Specimen Requirements

Respiratory Specimens

To improve diagnostic sensitivity, testing should be performed on multiple sample types.  Some studies have demonstrated the need for multiple samples collected over several days for optimal avian influenza detection. Given that most human cases have presented with lower respiratory tract infections, the collection of ONLY an upper respiratory specimen, particularly single nasopharyngeal or nasal swabs, is NOT recommended.  

  • At a minimum, collect a nasopharyngeal swab (nasopharyngeal wash or nasopharyngeal aspirate are also acceptable). For suspect avian influenza cases, oropharyngeal swabs may have better yield than nasopharyngeal specimens; an oropharyngeal swab should be performed preferentially if only one sample can be taken. However, if oropharyngeal specimens are collected, they should be accompanied by a specimen from the nasopharynx.

  • Place the swabs in a standard container with 2-3 ml of viral transport media (VTM). If the patient is hospitalized with pneumonia, specimens from the lower respiratory tract (e.g., tracheal aspirate, bronchoalveolar lavage) should also be obtained. In outpatient settings, it may be difficult to obtain samples from the lower respiratory tract of children. In these instances, two specimens from the upper respiratory tract (e.g. a nasopharyngeal wash and a throat swab) are acceptable. Use 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. Cotton or calcium alginate swabs are not acceptable for PCR testing.


  • For cases or contacts of cases with confirmed swine influenza, collect as much blood as possible (recommended volumes 3- 10 cc from children and 10-20 cc from adults) in a serum separator tube (red top or tiger top).  If possible, spin to separate sera before packaging.

Specimen Storage and Shipment

Specimens should be collected within the first 24-72 hours of onset of symptoms and no later than 5 days after onset of symptoms. The specimens should be kept refrigerated at 4ºC and sent on cold packs if they can be received by the laboratory within three days of the date collected. If samples cannot be received by the laboratory within three days, they should be frozen at -70 ºC or below and shipped on dry ice.

After review by the local health department, any requests for diagnostic testing at VRDL must be accompanied by the General Purpose Specimen Submittal Form (PDF)*. Local health departments may call CDPH-VRDL's Medical and Epidemiology Liaison Section at (510) 307-8585 for further assistance.

*The form must be filled out as completely as possible or the specimen will not be tested.
Specimens should be shipped per usual protocol to either your local public health laboratory or:

California Department of Public Health / VRDL  
ATTN: Specimen Receiving
850 Marina Bay Parkway   
Richmond, CA 94804     
(510) 307-8585

(510) 307-8578 (fax)

If the sample cannot be subtyped at the local public health laboratory, please alert VRDL by calling (510) 307-8585 and provide the estimated time of arrival and Tracking # for the shipment.


*If you are having difficulty accessing the General Purpose Specimen Submittal Form (PDF) please contact CDPH at (510) 307-8585 to request this information in an alternate format. We are currently in the process of converting this document to ADA web accessible formats. ​

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