NJ PHEL partners with the NJ 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 who have tested positive for influenza, COVID-19, or have influenza-like illness.  Submitted samples are tested at PHEL using a surveillance algorithm to help understand the prevalence of different viral diseases in the state, identify viral subtypes, and screen for genetic changes.  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 phel.influenza@doh.nj.gov.

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

NJ PHEL is closely monitoring the ongoing detections of and is able to perform diagnostic testing for Avian Influenza A(H5N1) virus.  Additional information about Avian influenza virus testing is located here: Avian Influenza Virus Testing

What samples should be submitted for Influenza testing at PHEL? 

• Immediately submit any influenza specimen that tests positive for influenza A but tests negative for seasonal influenza A subtypes [i.e., A(H1) and A(H3)] (a.k.a. Unsubtypeable influenza A).
  • There is no need for prior authorization to submit an unsubtypeable influenza specimen.
  • Specimens should be submitted to PHEL within 24 hours of obtaining subtyping results. 
  • Click here for more details regarding Unsubtypeable Influenza A

• Samples from patients with suspected novel influenza A virus infection
  • Novel influenza A virus refers to any influenza virus 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. 

• Additional samples may be requested by the NJ Communicable Disease Services, as a part of an outbreak investigation or for other respiratory surveillance efforts.

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 SARS-CoV-2 technical bulletin. 

For the most recent update of SARS-CoV-2 case rates and variant prevalence in NJ please see the Communicable Disease Services weekly Respiratory Illness Report

The preferred respiratory specimen type for most respiratory viral testing is a nasopharyngeal swab collected into 1-3 mL of viral transport media.   

• Additional specimen types may also be recommended based on the test requested.
  • PHEL accepts: Nasopharyngeal (NP) swabs, Conjunctival swabs, Oropharyngeal (OP) swab, Combined Nasopharyngeal and Oropharyngeal swabs, Nasal mid turbinate swabs, Anterior nasal swabs, Nasopharyngeal wash/aspirate, Nasal wash/aspirate, Bronchoalveolar lavage, tracheal aspirate, pleural fluid
    • Sputum and lung biopsy specimens may be accepted but cannot be tested at PHEL and will need to be forwarded to CDC for testing
• Refer to our Respiratory Specimen Collection Quick Guide for detailed instructions. 
• All swabs should be placed in a transport tube containing 1-3mL viral transport Media (VTM)
• Swab specimens should be collected using swabs with a synthetic tip (e.g., polyester or Dacron®) and an aluminum or plastic shaft.
• Submission of residual specimen volume is acceptable 

• Laboratories may also consider sending an aliquot (at least 0.5mL) in a secondary tube labeled with 2 patient identifiers (name and DOB) that is kept frozen.

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. 

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

If a delay in shipment to the laboratory is expected, store clinical specimens frozen at ≤-70°C and transport on dry ice.  

Maintaining temperature during transport is critical to maintaining specimen integrity.  Avoid freeze-thaw cycles.

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