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

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General Information

Lab Name
SARS CoV 2 (COVID 19) Qualitative PCR
Lab Code
NCVQLT
Epic Name
COVID-19 Coronavirus Qualitative PCR
Description

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

The laboratory performs three qualitative, one-step, Real-Time RT-PCR assays:

  • UW SARS-CoV-2 Real-Time RT-PCR Assay
  • Hologic Panther Fusion® PCR SARS-CoV-2 (COVID-2019) Emergency Use Authorization (EUA) Assay
  • Roche cobas® Qualitative PCR (510K) SARS-CoV-2 (COVID-2019) Assay

These assays are designed for the qualitative detection of SARS-CoV-2 nucleic acid in nasopharyngeal, oropharyngeal, and nasal swabs. Additionally, the UW SARS-CoV-2 Real-Time RT-PCR Assay is validated for cerebrospinal fluid (CSF), sputum, stool, plasma, bronchoalveolar lavage (BAL), and bronchial washings as valid specimen types. The Hologic Panther Fusion® SARS-CoV-2 Assay also accepts BAL and bronchial washings for testing.

SARS-CoV-2 is detected using Real-Time RT-PCR, a highly sensitive molecular technique that amplifies and detects viral RNA. This method targets specific regions of the SARS-CoV-2 genome, allowing for the qualitative identification of the virus in patient specimens. However, differences in assay design, sensitivity, and specimen type can influence detection. Refer to the methods section for detailed information on each individual assay, including target genes, and performance characteristics.

All test results must be interpreted in the context of clinical presentation, patient history, and epidemiological factors. Negative results do not preclude COVID-19 and should not be used as the sole basis for patient management decisions.

For inquiries: contact Client Support Services, available 24/7

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

References
Forms & Requisitions

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).

Synonyms
2019-nCoV, COVID, COVID-19, COVID19, nCoV, PUI nCoV, SARS, SARS-CoV-2, Wuhan Coronavirus
Components
Code Name
NCVSD SARS CoV 2 (COVID 19) Qual PCR Specimen Type
NCVRT SARS CoV 2 (COVID 19) Qual PCR Result
NCVINI SARS CoV 2 (COVID 19) Qual PCR Interpretation

Interpretation

Guidelines
Method

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 (510K) 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.

Reference Range
See individual components
References

Ordering & Collection

Specimen Type
nasopharyngeal (NP) or oropharyngeal (OP) swab, nasal swab, sputum, CSF, stool, plasma, or BAL
Collection

Acceptable Specimens:

Preferred sample types: Nasopharyngeal (NP) and oropharyngeal (OP) swab specimens

Other acceptable specimen types: Cerebrospinal fluid (CSF), Sputum/Endotracheal Tube (ETT), Stool, Plasma, Bronchoalveolar lavage (BAL), and Bronchial washings

Specimen Collection Guideline:

Collect nasopharyngeal (NP) and oropharyngeal (OP) swab specimens using a standard technique with a polyester-, rayon-, or nylon-tipped swab. Immediately place the swab into 3 mL of viral transport medium (VTM). Alternatively, swab specimens may be placed in saline or Liquid Amies.

The following VTM formulations have been verified for use:

  • Remel MicroTest M4, M4RT, M5, or M6 formulations
  • Copan Universal Transport Medium
  • BD Universal Viral Transport Medium

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.

Mixed specimens (nasal swab and OP swab) in one tube of VTM are okay. 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 the reliability of viral detection

Bronchoalveolar lavage (BAL) fluid and bronchial wash specimens should be collected using standard techniques.

Sputum/ETT collection: Obtain a specimen from a deep cough (preferably in the morning), induction, or intubation. Do not submit saliva.

Blood specimens: Only EDTA plasma or PPT are acceptable. Unacceptable specimens: Plasma from green-top (heparin), yellow-top (ACD), or gray-top (oxalate) tubes, as well as serum (no red-top tubes).

Stool specimens: A pea-sized sample must be collected in a clean container.

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.

Important Notes:

  • Leaking samples will not be processed.
  • At-home collected swabs cannot be accepted.
  • Orange Aptima Multitest Swab Transport Media tubes are not acceptable
Forms & Requisitions

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).

Handling Instructions

Send specimens to

UW Medicine
Department of Laboratory Medicine
Central Laboratory Annex

1602 Raymond 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

Quantity
Requested: 0.5mL
Minimum: 0.5mL

Processing

Receiving Instructions

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.
Misc Sendout

Performance

Lab Department
Central Lab Virology(RVIR)
Frequency
Test is performed multiple times a day; expect same-day results for specimens received in the morning, next-day otherwise.
Available STAT?
No
Performing Location(s)
CL Virology, Renton
206-685-6656

1602 Raymond Ave SW

Renton, WA 98057-3356

206-685-6656 opt 4

Billing & Coding

CPT Codes
87635
LOINC
94500-6
Regulatory Category
Laboratory-developed test
Interfaced Order Code
UOW3747