SARS-CoV-2 (COVID-19) Qualitative PCR

The UW Clinical Virology Laboratory in the Department of Laboratory Medicine and Pathology incorporates three assays for the detection of the COVID-19 virus (SARS-CoV-2) RNA.

Three qualitative one-step Real-Time RT-PCR assays; the UW SARS-CoV-2 Real-time RT-PCR assay, the Hologic SARS-CoV-2 Real-time RT-PCR assay and the cobas® SARS-CoV-2 assay.

All assays are intended for the qualitative detection of nucleic acid from SARS-CoV-2 in nasopharyngeal/oropharyngeal swabs and nasal swabs. CSF, Sputum, stool, plasma, and BAL are also acceptable specimens for the UW SARS-CoV-2 Real-time RT-PCR assay. When available, BAL and sputum have the highest positivity rates of any specimen type. Results are for the identification of SARS-CoV-2 RNA. Positive percent agreement: 100%. Negative percent agreement: 100%.

Important Notes:

• UW Laboratory Medicine Virology will prioritize maintaining clinically-actionable turnaround time for inpatient settings.
• Testing for inpatients or outpatients: Potential clients desiring to send tests to UW Virology contact CSS at 206-520-4600.
• Currently cannot accept at-home collected swabs and await further FDA guidance on this issue.

SARS-CoV-2 is detected by Real-time RT PCR: see methods for assay details.

Negative results do not preclude COVID-19 and should not be used as the sole basis for patient management decisions. Negative results must be combined with clinical observations, patient history, and epidemiological information.

The SARS-CoV-2 RNA is generally detectable in naso-/oropharynx during the acute phase of infection. If lower respiratory tract specimens are available such as BAL or sputum, they should be sent as they have a greater chance of detecting the virus. Positive results are indicative of active infection.

For all questions, contact Client Support Services (available 24/7):

Phone: (206) 520-4600 or 1 (800) 713-5198
Fax: (206) 520-4903
Email: commserv@uw.edu

Note: Due to supply chain variables and logistical workflows to minimize turn-around time, orders may be substituted for medically equivalent qualitative assays at an equivalent or cheaper cost. CPT/PLA codes may differ. Call the laboratory with questions.

SARS-CoV-2 is detected by using one of the following assays:

The UW SARS-CoV-2 Real-time RT-PCR assay targets two distinct regions within the N gene of SARS-CoV-2 (the causative agent for COVID-19). Amplification of both targets results in a presumptive positive (detectable) test result, while amplification of one of two targets results in an inconclusive result, and amplification of neither target results a negative (non-detectable) test result.

This test was developed and its performance characteristics determined by the University of Washington Department of Laboratory Medicine and Pathology. It has not been cleared or approved by the US Food and Drug Administration.

This laboratory is certified under the Clinical Laboratory Improvement Amendments (CLIA) as qualified to perform high complexity clinical laboratory testing. This test is used for clinical purposes. It should not be regarded as investigational or for research.

The Hologic Emergency Use Authorization (EUA) SARS-CoV-2 Real-time RT-PCR assay targets two conserved regions of the SARS-CoV-2 (the causative agent for COVID-19) ORF1ab gene. The two regions are not differentiated; amplification of either or both regions is a presumptive positive (detectable) test result and amplification of neither target results a negative (non-detectable) test result.

The Roche cobas SARS-CoV-2 Qualitative PCR Assay targets two regions of the SARS-CoV-2 (the causative agent for COVID-19) genome, the E gene and ORF1ab gene. Amplification of both targets results in a positive (detectable) test result, while amplification of one of two targets results in an inconclusive result, and amplification of neither target results in a negative (non-detectable) test result.

Acceptable Specimens and Media

• Prefer nasopharyngeal or oropharyngeal swab in Universal Transport Media (UTM) or viral transport medium (VTM).
• In cases where BAL and sputum are available, they should be sent as they have the highest positivity rates.
• Acceptable specimen types include nasopharyngeal or oropharngeal swab in UTM/VTM, nasopharyngeal swabs in M4 or M6 media, nasal swabs in UTM/VTM, ETT/sputum, BAL, CSF, plasma, and stool.
• If transport media is not available, place dry swabs in 2-3mL of PBS/sterile saline.
• Mixed specimens (nasal swab and OP swab) in one tube of VTM are okay.
• Orange Aptima Multitest Swab Transport Media tubes (Hologic SARS-CoV-2 assay only).
  • Forward all other Aptima collection tubes to Virology and Virology will determine if the tube is acceptable.

Collection

Instructions for Nasopharyngeal Swab: Gently insert mini-tipped flocked nasopharyngeal swab (swab on flexible plastic shaft) through the nostril and into the nasopharynx, reaching the posterior nasopharynx. Leave swab in place for 2-3 seconds then rotate completely around for 10-15 seconds. Remove swab and repeat the same process in the other nostril with the same swab.

After the second swab is completed, immediately place into the sterile vial containing media (UTM is preferred). Make sure that the swab is fully immersed in media, and that the shaft is short enough to completely tighten the cap. Obtaining columnar epithelial cells will enhance reliability of viral detection.

Instructions for Sputum: obtain specimen from deep cough (usually in AM), induction or intubation; do not send saliva.

Shipping

Send to the laboratory as soon as possible.

• Sample may be stored at 2 to 8°C for up to 72 hours of collection.
• Ship immediately to lab at 2 to 8°C (ice pack).
• If collection to receipt in the lab will exceed 72 hours freeze at -10°C or colder and ship on dry ice. Do not freeze/thaw.

• Aptima Multitest Swab Transport Media tubes may be stored at 2 to 8°C for up to 3 months of collection. Frozen samples are not acceptable.

Important notes

• Leaking samples will not be processed.
• Cannot accept at-home collected swabs and await further FDA guidance on this issue.

UW Medicine Locations

Place order in Epic using "COVID-19 Coronavirus Qualitative PCR" per routine.

Other Locations (eg, reference laboratory client)

Send all samples with the COVID-19 Test Requisition (form is a fillable pdf - please download and enter information before printing).

Send specimens to

UW Medicine
Department of Laboratory Medicine
Virology - Central Laboratory
1601 Lind Ave SW
Renton, WA 98057-3356
Tel: (206)-685-6656 opt 4

Additional information

Additional information on ordering, collection, and shipment can be found at https://depts.washington.edu/uwviro/order/

For all questions, contact Client Support Services (available 24/7):

Phone: (206) 520-4600 or 1 (800) 713-5198
Fax: (206) 520-4903
Email: commserv@uw.edu

Transport and store the tube at 2 to 25°C for up to 48 hours. Send to UW Virology Central Lab (Renton) via courier.

• Stability: Stable for 72 hours at 2 to 8°C.

Orange Aptima Multitest Swab Transport Media tubes

• Stability: Stable for 3 months at 2 to 8°C.