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HelpTest 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.
Secondary ID
614197Useful 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
Method Name
Reverse Transcription Polymerase Chain Reaction (RT-PCR) followed by Next-Generation Sequencing
Reporting Name
SARS-CoV-2 Lineage, Clade, S Mut, VSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time | |
|---|---|---|---|
| Varies | Frozen (preferred) | 14 days | |
| Refrigerated | 72 hours |
Clinical Information
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel, positive-sense, single-stranded RNA virus that causes COVID-19, and it contains an approximately 30,000 base pair long RNA genome that is prone to spontaneous genetic mutation. Worldwide scientific reports indicated emergence of specific variants of SARS-CoV-2 that are associated with increased transmissibility of this virus among susceptible humans, increased severity of disease, and/or reduced neutralization by vaccine-induced antibodies, therapeutic monoclonal antibodies, and convalescent plasma since December 2020.
A group of viruses within the same genus sharing the same distinctive set of mutations in the viral genome is called a variant. If enough mutations accumulate in a lineage, the viruses may evolve clear-cut differences in how they function. These lineages come to be known as strains. The United States SARS-CoV-2 inter-agency group, comprising the Department of Health and Human Services, Biomedical Advances Research and Development Authority, Centers for Disease Control and Prevention, Food and Drug Administration, National Institutes of Health, and Department of Defense, has developed a variant classification scheme that defines 3 classes of SARS-CoV-2 variants: variant of interest, variant of concern, and variant of high consequence (www.cdc.gov/coronavirus/2019-ncov/variants/variant-surveillance.html). The relative proportions of these variants present among the reported COVID-19 infections at the US national and state levels are available at www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-proportions.html.
A SARS-CoV-2 variant of interest contains specific genetic mutations that are associated with predicted increase in transmissibility or disease severity, possible impact on serologic and/or molecular diagnostic assays, and changes to the ACE2 receptor binding domain that may result in reduced neutralization by antibodies generated from previous infection or vaccination and reduced efficacy of monoclonal antibody therapy. Current SARS-CoV-2 variants of interest in the US are the B.1.525, B.1.526, and P.2 lineages, all of which share the D614G codon mutation in the S gene of the virus, and this mutation is associated with increased transmission of this virus.
A SARS-CoV-2 variant of concern contains specific genetic mutations that are associated with increase in transmissibility, severe disease (increased hospitalization or death), failures of serologic and/or molecular diagnostic assays, and significant reduction in neutralization by antibodies generated from previous infection or vaccination, and reduced efficacy of monoclonal antibody therapy or vaccines. Current SARS-CoV-2 variants of interest in the US are the B.1.1.7, B.1.351, B.1.427, B.1.429, and P.1 lineages.
A SARS-CoV-2 variant of high consequence has clear evidence of significantly reduced effectiveness of current preventive measures, therapeutic agents, and medical interventions, when compared to previously circulating variants. At present, there are no such variants in US or globally.
Reference Values
Not applicable
Cautions
The ability to amplify the SARS-CoV-2 target sequences and detect S gene mutations with this assay is limited in specimens with viral polymerase chain reaction target cycle threshold values of greater than 30.0 (ca. <50,000 copies/mL).
Viral variants present at less than 50% of the total viral population in a given clinical specimen will not be detected with this assay, as the nucleic acid substitution detection threshold is set at 50%.
Day(s) Performed
Varies
Report Available
2 to 10 daysPerforming 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. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
87913