Respiratory Virus Testing Information

Collection of samples

Collection kit: BD Universal Viral Transport Kit: 3 mL with a regular and flexible minitip flocked swab. Studies have shown that the flocked swabs have a higher sensitivity for detection of pathogens. Although the flocked swab kits are preferred, other equivalent viral transport kits will still be accepted.

Where can I get this kit?

HUP: stocked by HUP Storeroom, Ravdin Basement [Lawson code 195443]

PA Hospital: 8 AM-8 PM Mon thru Fri and 8 AM-4 PM Sat & Sun kits available in Serology/Microbiology (215-829-3555); at other times from Central Lab on 6th floor (215-829-3557)

PPMC: kits are stocked in STAT lab, W552 Wright-Saunders (215-662-9280)

CPUP: kits are stocked in CAM building (Phlebotomy) and at 3701 Market (6th floor Phlebotomy station)

CCA: Audrey Baylock will handle orders and can be contacted via global email or 215-615-2069

Note: The BD Liquid Amies Elution Swab (ESwab) collection kit (BD 220245; Lawson 202586) is used for MRSA screening and routine bacterial culture. Although similar in appearance to the BD Universal Viral Transport kit, they are not interchangeable.

Sample type: The optimal specimen for viral studies is a nasopharyngeal (NP) swab, which should always be taken if possible. Yield can be increased by also taking a throat swab and combining both into the single tube of viral transport medium. If a NP swab cannot be collected, then collect just a throat swab. Anecdotal evidence suggests that the testing of bronchoalveolar lavage specimens may improve clinical sensitivity for detection of some subtypes of influenza virus such as 2009 A (swine origin) H1N1, submission of a BAL specimen (minimum 5 ml, optimum 10-15 ml) may be preferred to a combined throat/NP swab, if a BAL specimen is available.

How to collect: Healthcare providers obtaining the specimens should use contact precautions (gown, glove, eye protection) and wear a surgical mask for nasopharyngeal and oropharyngeal swabs; however an N95 mask is required for suctioning/obtaining a tracheal aspirate. The NP swab is collected using the minitip swab with flexible shaft contained in the collection kit, and the throat swab using the regular flocked swab. Any unused swab should be discarded. Do not perform this procedure on anyone with recent injury or surgery to the nasopharyngeal area. Do not use any swabs that are not provided with the collection kits as these could produce false-negative results, especially those swabs made of wood or cotton. Refer to picture at right.

Collection of the Nasopharyngeal Specimen

1. Remove the minitip swab with flexible shaft from the wrapper.
2. Tilt patient’s head back and insert the swab gently and laterally through one nostril avoiding turbinates.
3. Rotate swab over surface of posterior nasopharynx.
4. Repeat procedure in 2nd nostril using same swab.
5. Insert swab into the vial with the medium and break the shaft by bending it against the vial wall evenly at the pre-scored line.
6. Continue with collection of throat specimen (below) if desired.

Collection of the Throat Specimen

1. Remove the regular flocked swab from wrapper.
2. Rub the swab against the patient’s tonsillar mucosae and posterior orpharynx.
3. Place the swab in the same tube of viral transport medium as the NP sample and break the shaft by bending it against the vial wall evenly at the pre-scored line.
4. Replace cap on medium vial and close tightly.
5. Label vial with patient identifiers and send to laboratory

Transport of samples: Samples should be delivered to the HUP Central Receiving Lab on 7 Founders. If a sample is unable to be transported immediately it should be placed at 4°C.

HUP: Pneumatic tube (station number 01) or via courier. Hand deliver BAL specimens promptly after collection.

PAH: Deliver to PAH Central Specimen Processing on 6 Preston for transport to HUP. At PAH samples can be sent to Tube station number 64. BAL specimens should be hand delivered promptly after collection.

PPMC: Samples should be delivered to the Stat lab Room W552 Wright Saunders Bldg. BAL specimens should be hand delivered promptly after collection.

Ordering the test

The test code for Epic and Sunrise ordering is “Respiratory Virus Molecular Detection.”

For Cerner Millenium, the test code is “RVPCR”

Hand written requisitions will also be accepted. Specify: “Respiratory Virus Molecular Testing.”

Testing information

Where is testing performed?

Testing is performed in the Molecular Pathology Laboratory located on 7 Gates and 7 Maloney in HUP.

What method is used and what viruses does it detect?

Real-time reverse transcription PCR (RNA virus) or real time PCR (DNA virus) is used to detect the presence of any of the following viruses (influenza A; influenza B; respiratory syncytial virus types A and B; parainfluenza virus types 1, 2, and 3; adenovirus and human metapneumovirus). Data suggests that this assay can detect the 2009 H1N1 influenza virus, however it cannot be distinguished from other influenza A virus subtypes. Additional subtyping of Influenza A will not routinely be performed, but the need will be reevaluated as the season progresses.

When is the test performed?

Testing is currently performed daily Monday through Saturday. Additional weekend testing will be offered as the need arises during the flu season. Depending on volume additional changes in schedule may be made. Therefore, please call the lab if you have any questions or concerns. The cut-off time for same day testing is receipt of the sample in HUP Central Receiving by 8 AM.

Getting results

Where will results be available?

Results will be viewable in Epic, Medview, and Sunrise information systems. Positive results on in patients and some outpatients will be communicated to infection control, who will then contact the clinician submitting the specimen.

When will results be available?

Although unanticipated delays may occur, we expect that most results will be available by 4-6 PM each day for specimens received before 8 AM of the same day. Specimens received after 8 AM will be reported by 4-6 PM the following day.

Where can I get more information or get help with an urgent issue?

Between the hours of 8 AM to 8:30 PM please call the Molecular Pathology Laboratory at 215-662-6121.

Clinical questions should be addressed to the Molecular Pathology resident at pager 215-980-9868 between the hours of 8 AM to 5 PM weekdays. On weekends and after 5 PM on weekdays, the Clinical Pathology resident on-call should be paged at 215-306-0286.

updated 9/7/16 PE