COVID-19 Community Levels Map Update, Dec. 2, 2022: The Centers for Disease Control and Prevention has listed Fairfield, Hartford, Litchfield, Middlesex, New Haven, Tolland, and Windham Counties in the Medium/Yellow category as part of its COVID-19 Community Levels Map. New London County is currently listed in the Low/Green category. Visit the CDC COVID-19 Community Levels Map for updates.

Laboratory Instructions for Influenza Testing and Surveillance, 2021-2022 Season

Influenza PCR Testing Kit Collection Instructions

Testing and treatment of influenza when SARS-CoV-2 and influenza viruses are co-circulating

To monitor circulating influenza strains throughout the ongoing  dual influenza season/COVID-19 pandemic, rapidly identify novel strains, and determine the effectiveness of this season’s vaccines, the Connecticut Department of Public Health (DPH), State Public Health Laboratory (SPHL) provides testing of specimens obtained from select patients. During the COVID-19 pandemic, most patients presenting with respiratory symptoms had been tested for the SARS-CoV-2 virus prior to any testing for influenza or other respiratory viruses.

For the 2021-2022 influenza season and throughout the year, laboratories are asked to submit respiratory specimens obtained from patients with a positive or unknown influenza test result AND a negative COVID test result* in the following categories (1-4) who present with influenza-like illness (ILI= fever ≥100°F [37.8°C] AND cough and/or sore throat).  Respiratory specimens may also be accepted from patients with a positive influenza test result AND a positive COVID test result* who present with ILI in the following categories:

  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, contact the DPH EEIP at 860-509-7994**);
  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.

*During the dual 2021-2022 influenza season/COVID-19 pandemic, SPHL will also consider accepting specimens from patients who may not yet have been tested for SARS-CoV-2 or who have tested positive for both influenza and COVID to evaluate for combined influenza/COVID-19 infections. The SPHL will utilize the CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay for their primary evaluation of specimens from patients presenting with ILI. Since the SPHL has limited resources for testing using this assay, requests for multiplex testing beyond typical seasonal influenza surveillance testing must be approved by DPH EEIP at 860-509-7994 prior to specimen submission.

** Please contact the DPH Epidemiology and Emerging Infections Program (EEIP) at 860-509-7994 (or 860-509-8000 on evenings/weekends/holidays) to discuss respiratory viral panel (RVP) testing or testing for suspect avian influenza or MERS prior to submitting specimens.

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.


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 below.


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).

Notes: The SPHL testing options described here should be considered part of DPH disease surveillance, and not as diagnostic testing services. These testing criteria are subject to change based on the evolving nature of the dual influenza season/COVID-19 pandemic and the presence of other emerging respiratory viruses.

Influenza/COVID-19 PCR Testing Kit Collection Instructions

1. The contents of the kit include:

a.  M4RT viral transport tube (universal transport medium, Amies transport medium (eSwab), or sterile saline are also acceptable);

b.  Nasopharyngeal or 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 ensure 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/COVID-19 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 completed 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 02/23/2022.