Criteria for Submitting Specimens for Influenza and SARS-CoV-2 Testing and Surveillance, 2023-2024 Season

Influenza/COVID-19 PCR Testing Kit Collection Instructions

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


To monitor circulating COVID-19 and influenza strains, 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 for surveillance. For the 2023-2024 viral respiratory disease season and throughout the year, laboratories are asked to submit respiratory specimens from patients with symptoms of a respiratory disease according to the following criteria:

1) Ten (10) specimens per week for patients with Influenza

  • Hospitalized patients with confirmed influenza
  • 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 Tract Microbiota panel (RTM) testing for enterovirus and other respiratory viruses.
  • 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**).

2) Ten (10) specimens per week for patientwith COVID-19

  • Hospitalized patients with confirmed COVID-19

3) 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.

** 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 Tract Microbiota panel (RTM) testing or testing for suspect avian influenza or MERS prior to submitting specimens.


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 AMD Laboratory at 860-920-6689.


The entire "Specimens for Influenza and SARS-CoV-2 Variant Analysis" surveillance form must be completed for SPHL to accept specimens. This form must be used when submitting for all surveillance specimens.


If testing is required for Influenza or SARS-CoV-2, then the entire “Clinical Test Requisition” (OL-9B form) must be completed for SPHL to accept specimens for testing.


Influenza/SARS-CoV-2 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 specimen transportation: Category B Infectious Substance insulated box (Saf T Pak STP 309)

2.  Complete all required fields on the "Specimens for Influenza and SARS-CoV-2 Variant Analysis" surveillance form OR the “Clinical Test Requisition (OL-9B 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.

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

5.  For 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. For respiratory specimens, submit at least 2 mL liquid specimen in a sterile screw capped container.
f. For both respiratory and swab specimens, place them in the sealable biohazard bag containing the absorbent pad. One specimen per biohazard bag.
g. Seal the top of the plastic bag.
h. Insert biohazard bag into white Tyvek bag and seal.
i. Place a frozen ice pack, white Tyvek bag, and completed surveillance form into the insulated transport box (Category B box).
j. Seal the transport box for transportation. Be sure to include submitter's telephone number on outer box.

To request Influenza/SARS-CoV-2 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 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 -70°C and sent to the SPHL on dry ice to remain frozen while in transit. If dry ice is not available, ice packs can be used instead. Specimens not collected, handled, or transported in the prescribed manner may yield inaccurate results and will be rejected for testing.


This page last updated 10/03/2023.