Respiratory Viruses

COVID-19 Testing

The molecular virology unit uses NAAT (nucleic acid amplification testing) methods to detect SARS-CoV-2 (the virus which causes COVID-19) for both diagnostic and surveillance purposes, including variant identification.   

Variant identification is performed for surveillance purposes only, and individual diagnostic results cannot be returned to providers.  For current specimen submission guidance, see our technical bulletin. 

For the most recent update of SARS-CoV-2 case rates and variant prevalence in NJ please see the Communicable Disease Services website: 

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Influenza Testing

The molecular virology unit uses real time RT-PCR (reverse transcriptase-polymerase chain reaction) to detect novel influenza, as well as all seasonal strains of flu in clinical samples.  

What samples should be submitted for Influenza at PHEL? 

  • Immediately submit any influenza sample that is UNSUBTYPEABLE with a molecular influenza assay that can detect currently circulating influenza A virus subtypes (i.e., “seasonal influenza” subtypes) 
  • For example, results that indicate “influenza A positive”, but with subtype not identified. 
  • Do not submit specimens which are not tested for influenza subtype, or specimens which are inconclusive for influenza infection. 
  • Novel influenza A virus refers to any influenza specimen which is not known to circulate seasonally in humans, including avian influenza viruses (e.g. H5N1 or H7N2), or swine variant influenza viruses. 
  • Refer to current guidelines and contact your local health department if a patient meets the case criteria for a suspect novel influenza A virus infection to get approval to send specimens to PHEL. 
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Respiratory Virus Surveillance Program

PHEL partners with the NJDOH Communicable Disease Service (CDS) to perform influenza and non-flu respiratory viral surveillance throughout the state.  A network of sentinel providers submits clinical samples to PHEL from patients with influenza-like illness which are tested with a surveillance algorithm covering a panel of viral disease.  If you are interested in becoming a sentinel surveillance provider for the NJ Respiratory Virus Surveillance program, please contact us for more information by emailing

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Preferred Respiratory Specimens

The preferred respiratory specimen type for most respiratory viral testing is a nasopharyngeal swab collected into viral transport media.   

  • Additional specimen types (such as nasal swabs, oropharyngeal swabs, combined swabs, nasal washes or aspirates, or lower respiratory specimens) may also be recommended based on the test requested. 
  • 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 sterile viral transport medium (VTM). 
  • Refer to the technical bulletin “How to Collect a Nasopharyngeal Swab” for detailed instructions. 

Always refer to the associated technical bulletins for your test request for the most up-to-date list of recommended specimen types and collection guidance. 

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Storing and Shipping Clinical Specimens to PHEL

After collection specimens should be placed at 4°C (refrigerator) and shipped on ice packs if the sample is to be shipped immediately (within 72 hours of collection). 

If a delay in shipment to the laboratory is expected, store clinical specimens at ≤-20°C (for no more than 7 days) or at ≤-70°C and transport on dry ice.  

Avoid freezing and thawing specimens because viability of some viruses which were frozen and then thawed is greatly diminished.  All specimens should be labeled clearly and include a printed paper requisition form with all required information in the package. 

Click here for more information regarding Shipping Specimens to PHEL

Click here for more information regarding Shipping Infectious Specimens

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Last Reviewed: 12/10/2023