Laboratory Instructions for Influenza Testing and Surveillance, 2019-2020 Season


Influenza PCR Testing Kit Collection Instructions

To monitor circulating influenza strains throughout the season, rapidly identify novel strains, and determine the effectiveness of this season’s vaccines, the Connecticut Department of Public Health, State Public Health Laboratory (SPHL) provides testing of specimens obtained from select patients. For the 2019-2020 influenza season, please submit respiratory specimens obtained from the following patients who present with influenza-like illness (ILI= fever ≥100°F [37.8°C] AND cough and/or sore throat), regardless of rapid antigen testing status.

  1. All hospitalized patients with ILI or confirmed influenza;
  2. Selected non-hospitalized patients with ILI including: a) patients of ILI network (ILINet) providers, b) patients associated with outbreaks in long-term care, schools, or other facilities, and c) in children, severe respiratory illness with or without fever. Please contact the DPH Epidemiology and Emerging Infections Program (EEIP) at 860-509-7994 to discuss testing of 2a-c, including possible respiratory viral panel (RVP) testing for enterovirus and other respiratory viruses; 
  3. All patients with ILI and recent close exposure to swine, sick poultry at farms and agricultural settings, or migratory birds (exposure history should be provided);
  4. All patients with pneumonia and/or Acute Respiratory Distress Syndrome (ARDS) developing within 17 days of travel to Southeast Asia or within 14 days of travel in or near the Arabian Peninsula, contact the DPH EEIP at 860-509-7994 regarding possible avian flu or Middle East Respiratory Syndrome Coronavirus [MERS-CoV] testing. Travel history should be provided.

The sensitivity of rapid influenza diagnostic tests (RIDTs) and direct immunofluorescence assays (DFAs) are lower than real-time reverse transcriptase polymerase chain reaction (rRT-PCR) tests and viral culture. A negative RIDT or DFA result does not rule out influenza virus infection. Moreover, these tests cannot distinguish between influenza A subtypes, such as the 2009 H1N1 or H3N2 influenza A viruses. For additional information visit the CDC website.

Please also note that federal guidelines requiring specimens to be transported on ice or with ice packs remain in effect. For questions or assistance regarding collection and handling of specimens, please call the SPHL Virology Laboratory at 860-920-6662. Influenza PCR specimen collection kits can be ordered by calling Support Services at 860-920-6674 or 860-920-6675. See additional specimen collection and shipping instructions on the following page.

The entire Clinical Test Requisition form (OL-9B) must be completed in order for the SPHL to accept specimens for influenza testing.  Please provide reasons for testing including ILI symptoms, hospitalization, outbreak association, close exposure to swine, poultry or other birds, and/or international travel history in the “Comments” space (see Section 3 of the OL-9B).

Note: These criteria are subject to change based on the evolving nature of the influenza season and the presence of emerging respiratory viruses.


Influenza PCR Testing Kit Collection Instructions

1. The contents of the kit include:

a.  M4RT viral transport tube;

b.  Nasopharyngeal and a sterile polyester-tipped sampling swab (Note: specimens collected using Calcium alginate swabs or swabs with wooden shafts are unacceptable for testing);

c.  Cold pack (place in freezer to insure that it is ready for future use);

d.  For specimens being mailed via overnight carrier: Category B Infectious Substance insulated box

2.  Complete all required fields on the Clinical Test Requisition form (OL-9B). Include reason for testing, symptoms, travel history, and rapid antigen flu test results on the form.

3.  Label the collection container with:

a.  Patient name

b.  Date of birth

c.  Date of collection

d.  Specimen source. Preferred specimen sources include: a) Nasopharyngeal or oropharyngeal swab submitted in viral transport media, b) Respiratory specimens such as bronchoalveolar lavage, tracheal aspirates, sputum, nasopharyngeal or oropharyngeal aspirates or washes. Submit at least 2 mL liquid specimen in a sterile screw capped container.

4.  Obtain an appropriate respiratory specimen from the patient using the proper collection technique.

5.  For nasopharyngeal or oropharyngeal specimens:

a.  Remove the screw cap top from the labeled M4RT viral transport tube.

b.  Insert the swab into the labeled M4RT tube until the swab touches the bottom.

c.  Break or cut off any excess swab handle and discard.

d.  Replace the cap on the labeled M4RT viral transport tube and firmly tighten.

e.  Place the labeled M4RT tube in the sealable biohazard bag containing the absorbent pad.

f.  Seal the top of the plastic bag.

g.  Place the completed OL-9B form in the outer pocket of the biohazard specimen bag.

6. For transport via same-day courier:

a.  Submit the specimen in the sealed biohazard bag containing the absorbent pad.

b.  Place this bag inside a rigid outer container with a frozen ice pack.

7.  For transport via overnight carrier:

a.  Insert biohazard bag into white Tyvek bag and seal.

b.  Place the frozen ice pack, white Tyvek bag, and complete OL-9B form into the insulated transport box.

c.  Seal the transport box for shipping. Be sure to include submitter's telephone number on outer box.

d.  Ship the box to the State Public Health Laboratory (SPHL) via overnight carrier.


To request Influenza PCR specimen collection kits, please email: or call 860-920-6674 or 860-920-6675.


NOTE: Specimens transported with an ice pack must be maintained at 35°F-46°F [2°-8°C] and received at the SPHL within 72 hours of collection. If it is anticipated that specimens will not be delivered within 3 days, they must be frozen at -94°F [-70°C] and shipped to the SPHL on dry ice to remain frozen while in transit. Specimens not collected, handled, or transported in the prescribed manner may yield inaccurate results and will be rejected for testing.




This page last updated 10/07/2019.