Respiratory viruses (multiplex panel)

Microbiology
Virology
○ Nasopharyngeal swab ○ Throat swab ○ Sputum ○ BAL ○ Bronchial washings ○ Pleural fluid ○ Tracheal aspirates ○ Tissue (respiratory)
Other Information
○ This will be referred to the Public Health Ontario Laboratory. Their assay will detect the following respiratory viruses: influenza A, influenza A H3 subtype, influenza A H1 (pdm09) subtype, influenza B, respiratory syncytial virus (RSV A/B), parainfluenza (1 –4), adenovirus, enterovirus, seasonal human coronavirus (OC43, 229E, NL63, HKU1), rhinovirus and human metapneumovirus.
○ This test will be performed on eligible persons only: 1) symptomatic children (<18 years) seen in the ED, 2) symptomatic hospitalized patients or residents in institutional settings, 3) specimens from the first four symptomatic individuals in an outbreak setting.
○ NP swabs is the most sensitive specimen type for respiratory virus testing.
○ To know which patient populations are eligible for testing at UHN/SH Microbiology Laboratory, see Respiratory pathogens
○ For SARS-CoV-2 testing only, see: SARS-CoV-2, severe acute respiratory syndrome coronavirus - detection
○ NP/throat swab: single swab in universal transport medium
○ Sputum/BAL/bronchial washings/aspirates/pleural fluid/tissues: sterile container (1mL)

Nasopharyngeal swab
○ Insert tip of swab into nostril aiming along the floor of nasal cavity until posterior wall of nasopharynx is reached. Resistance will be felt when reached. Rotate swab for 10-30s. Place swab into transport medium and close tube. Repeat collection with second nostril.
Throat swab:
○ Collect the specimen using a clean, sterile swab by swabbing the posterior oropharynx vigorously and placing it in universal transport medium.

Sputum:
○ Collect sputum by expectoration or induction in a sterile container.

BAL
○ Pass bronchoscope transnasally or transorally (if patient is not intubated) or via endotracheal tube (if patient is intubated). Instill a large volume of 0.85% sterile saline (nonbacteriostatic) into the airway lumen. Discard the initial fluid recovered (likely contaminated). Collect remaining fluid in a clean, sterile container via suction.

Bronchial washing/brush specimens
○ Pass bronchoscope transnasally or transorally (if patient is not intubated) or via endotracheal tube (if patient is intubated). For washings, inject aliquots of approximately 20 to 30 mL of 0.85% sterile saline (nonbacteriostatic) for adults or 5 mL for children. Suction washings into a sterile container.
○ For brushings, instill brush to collect cellular material from bronchial epithelial wall. Place protected brush sample (cut off approximately 30-40mm from the end of the brush) in sterile container with 1 mL of saline.

Tracheal aspirates
○ Samples should be collected aseptically through decontaminated skin using a syringe and needle and placed in a sterile container and submitted to the laboratory ASAP.

Pleural fluid
○ Decontaminate skin. Insert needle into pleural space, aspirate fluid into syringe OR collect pleural fluid directly from drain if chest tube has been inserted to drain pleural space. Transfer specimen (min volume 1 mL) into sterile, leakproof container

Tissue (Respiratory tract)
○ Collect 5-10 mm3 tissue aseptically using surgical technique. Place in a clean, sterile container with a small amount of sterile saline.

Refer to section Sample Processing / Delivery
In-house ( qualified based on criteria) PHOL - not qualified
○ Up to 4 days
416-586-4800 extension 4621
NO
○ Label specimen container. Place specimens in biohazard bag and seal.

○ Specimens should be stored and transported to the laboratory at refrigeration temperature (2-8C˚) immediately after collection.

○ The specimen will be referred* to Public Health Ontario Laboratory for multiplex PCR testing

* Testing on specimens from select inpatients will be performed in house