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Test ID COVNG Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage, Clade, and Spike Gene Mutation Detection, Next-Generation Sequencing, Varies


Ordering Guidance


This test should only be requested on known SARS-CoV-2 RNA-positive upper or lower respiratory tract specimens, with polymerase chain reaction target cycle threshold value of to 30.0 or less or transcription-mediated amplification generated relative light units of 1200 or more.

 

This test should not be used to detect the presence or absence of SARS-CoV-2 in an individual, with or without symptoms or signs of COVID-19. For these cases, order COVOO / Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA Detection, Varies.



Shipping Instructions


Ship specimens refrigerated (if <72 hours from collection to arrive at Mayo Clinic Laboratories [MCL]) or frozen (if 72 hours or more from collection to arrive at MCL)



Necessary Information


The following question must be answered at the time of test ordering:

Does the patient have a positive SARS-CoV-2, COVID19 polymerase chain reaction test result within the last 5 days? Answer "Yes" or "No".

Note: Test orders for submitted specimens with a "No" answer to this question will be canceled.



Specimen Required


Call 800-533-1710 to have this test added to a previously collected specimen that tested positive for SARS-CoV-2, COVID19 with COVOO, COVID, or COFLU. A new specimen would not be needed if there is sufficient specimen volume remaining.

 

Specimen Type: Nasopharyngeal (NP), oropharyngeal (OP ie, throat), nasal mid-turbinate, or nares/nasal swab

Supplies: Swab, Sterile Polyester(T507)

Collection Container/Tube:

Preferred: Sterile polyester swab

Acceptable: Dacron-tipped swab with plastic shaft

Submission Container/Tube: Universal transport media, viral transport media, or equivalent (eg, Copan UTM-RT, BD VTM, MicroTest M4, M4-RT, M5). Media should not contain guanidine thiocyanate (GTC).

For more information on acceptable transport media, see www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testing-sars-cov-2

Specimen Volume: Entire specimen with a minimum of 1.5 mL (maximum 3 mL) of transport media

Collection Instructions:

1. Collect specimen by swabbing back and forth over nasal or pharyngeal mucosa surface to maximize recovery of cells.

2. NP and OP swab specimens may be combined at collection into a single vial of transport media but only 1 swab is required for analysis.

3. Swab must be placed into transport medium. Swab shaft should be broken or cut so that there is no obstruction to the sample or pressure on the media container cap.

4. Do not send in glass tubes, vacutainer tubes, or tubes with push caps.

5. Do not overfill with more than 3 mL total volume of media.

 

Specimen Type: Nasopharyngeal aspirate or nasal washings

Container/Tube: Sterile container

Specimen Volume: Minimum of 1.5 mL

Additional Information: Do not aliquot into viral transport media, glass tubes, vacutainer tubes, or tubes with push caps.

 

Specimen Type: Nasopharyngeal aspirate or nasal washings, bronchoalveolar lavage (BAL) fluid, bronchial washings, endotracheal aspirate, sputum

Container/Tube: Sterile container

Specimen Volume: Minimum of 1.5 mL

Additional Information: Do not aliquot into viral transport media, glass tubes, vacutainer tubes, or tubes with push caps.


Useful For

Distinguishing between persistent infection with the same viral strain and reinfection with a new viral strain in an individual with recurrent positive molecular test results for SARS-CoV-2

 

Detection and identification of vaccine-escape SARS-CoV-2 variants with spike (S) gene variant of interest

 

Detection and identification of SARS-CoV-2 variants containing S gene variants of interest that reduce the efficacy of vaccine-induced antibodies, convalescent plasma, and/or monoclonal antibody therapy for COVID-19

 

Detection and identification of SARS-CoV-2 variants containing RdRp codon mutations of interest that reduce the efficacy of nucleoside analogs used in the therapy of COVID-19

Highlights

This test uses polymerase chain reaction (PCR) to amplify multiple SARS-CoV-2 genetic sequences covering 99.9% of the viral genome, followed by a next-generation sequencing assay with sequence analyses to determine the Pangolin lineage, Nextclade clade assignment, and alterations of the viral spike (S) protein and RdRp encoding codons in known SARS-CoV-2 RNA-positive respiratory tract specimens. Testing is more likely to be successful in positive specimens with PCR target cycle threshold values of 30.0 or less, or transcription-mediated amplification generated relative light units of 1200 or more.

Method Name

Reverse Transcription Polymerase Chain Reaction (RT-PCR) followed by Next-Generation Sequencing

Reporting Name

SARS-CoV-2 Lineage, Clade, S Mut, V

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Frozen (preferred) 14 days
  Refrigerated  72 hours

Reference Values

Not applicable

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

87913

LOINC Code Information

Test ID Test Order Name Order LOINC Value
COVNG SARS-CoV-2 Lineage, Clade, S Mut, V 96894-1

 

Result ID Test Result Name Result LOINC Value
614373 SARS-CoV-2 PANGO lineage 96895-8
614421 SARS-CoV-2 Nextstrain clade 96896-6
614374 S codon mutations of interest 96751-3
614501 S mutations of unknown significance 96751-3
616432 RdRp codon mutations of interest 99314-7
616433 RdRp mutations of unknown significance 99314-7
CVNGS SARS-CoV-2 Specimen Source 31208-2
CVNGR Patient Race 72826-1
CVNGE Patient Ethnicity 69490-1
CVPOS Recent Positive PCR Result within 5 days? 86955-2

NY State Approved

Yes

Day(s) Performed

Varies

Report Available

2 to 10 days