Test Catalog

Test Id : COVNG

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

Useful For
Suggests clinical disorders or settings where the test may be helpful

Distinguishing between persistent infection with the same viral strain and re-infection with a new viral strain in an individual with recurrent positive molecular test results for severe acute respiratory syndrome coronavirus 2 (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

Highlights

This test uses polymerase chain reaction (PCR) to amplify multiple severe acute respiratory syndrome coronavirus 2 (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-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 (Ct) values of 30.0 or less, or transcription-mediated amplification generated relative light units (RLU) of 1200 or more.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

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

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

No

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

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

Aliases
Lists additional common names for a test, as an aid in searching

Coronavirus

COVID

COVID Variant

COVID-19

S gene mutation

SARS

SARS-CoV-2

SARS-CoV-2 clade

SARS-CoV-2 lineage

SARS-CoV-2 variant

Next Gen Sequencing

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

This test should only be requested on known severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-positive upper or lower respiratory tract specimens, with polymerase chain reaction target cycle threshold (Ct) 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 coronavirus disease 2019 (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 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 severe acute respiratory syndrome coronavirus 2019 (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
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Call 800-533-1710 to have this test added to a previously collected specimen that tested positive for severe acute respiratory syndrome coronavirus 2019 (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, 10 per package (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. For more information on OP swab specimen collection, see COVID-19 Oropharyngeal Collection Instructions in Special Instructions.

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.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Calcium alginate-tipped swab, wooden shaft swab, or swab collection tubes containing gel or charcoal additive
Transport media tubes containing the entire swab (shaft and knob attached)
Glass transport media tubes
Bloody specimen
Reject
Thawed Cold OK; Warm reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

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

Useful For
Suggests clinical disorders or settings where the test may be helpful

Distinguishing between persistent infection with the same viral strain and re-infection with a new viral strain in an individual with recurrent positive molecular test results for severe acute respiratory syndrome coronavirus 2 (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

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel, positive-sense, single-stranded RNA virus that causes coronavirus disease of 2019 (COVID-19), and it contains 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 (US) 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/cases-updates/variant-surveillance/variant-info.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 (RBD) 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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Not applicable

Interpretation
Provides information to assist in interpretation of the test results

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific S gene mutations are detected with this assay at a minimum 50% frequency for detecting codon substitutions in the viral sequence.

 

An "Inconclusive" result indicates that testing failed due to poor sequence quality resulting from the presence of inhibitory substances and/or low amount of virus (ie, polymerase chain reaction [PCR] target cycle threshold [Ct] value of >30.0) present in the submitted specimen. A new specimen should be collected and submitted for retesting if clinically necessary.

 

The table below indicates the clinical implications of known SARS-CoV-2 variants of interest and variants of concern:

 

SARS-CoV-2 PANGO lineage

WHO label

Disease severity

Efficacy of convalescent plasma therapy

Efficacy of monoclonal antibodies(a)

Efficacy of Pfizer/BioNTech mRNA vaccine

Efficacy of Moderna mRNA vaccine

Efficacy of J and J adenovirus vaccine

B.1.1.7

Alpha

No effect

Good

Good

Good

Good

Good

B.1.351

Beta

Increased

Reduced

Reduced(b)

Reduced

Reduced

Good

B.1.427

Epsilon

Unknown

Reduced

Reduced(c)

Reduced

Reduced

Reduced

B.1.429

Epsilon

Unknown

Reduced

Reduced(c)

Reduced

Reduced

Reduced

B.1.525

Eta

Unknown

Reduced

Reduced(d)

Reduced

Reduced

Reduced

B.1.526

Iota

Unknown

Reduced

Reduced(d)

Reduced

Reduced

Reduced

B.1.617.1

Kappa

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

B.1.617.2

Delta

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

B.1.621

Mu

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

C.37

Lambda

Unknown

Unknown

Unknown

Unknown

Unknown

Unknown

P.1

Gamma

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

P.2

Zeta

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

P.3

Theta

Unknown

Reduced

Reduced(b)

Unknown

Unknown

Unknown

 

a. Based on in vitro (experimental) data only

b. Reduced efficacy of bamlanivimab, etesevimab, and casirivimab

c. Reduced efficacy of bamlanivimab

d. Reduced efficacy of bamlanivimab and casirivimab

 

The table below indicates the clinical implications of known codon-substitutions in the SARS-CoV-2 spike protein (S) encoding region: 

S codon mutation of interest

Effect on viral transmission and infectivity

Effect on severity of disease

Efficacy of convalescent plasma therapy

Efficacy of monoclonal antibodies*

Efficacy of vaccines

H69-V70 deletion**

Increased

Unknown

No effect

No effect

No effect

G142D

Increased

Increased

Reduced

Reduced for bamlanivimab

Reduced

Y144 or Y145 deletion

Unknown

Unknown

No effect

No effect

No effect

E156-F157 deletion

Unknown

Unknown

Reduced

Reduced for bamlanivimab

Reduced

G158R

Unknown

Unknown

Reduced

Reduced for bamlanivimab

Reduced

Q409E

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

K417E, K417N, K417R, K417T

Increased

Unknown

Unknown

Reduced for casirivimab, etesevimab

Unknown

D420N

Unknown

Unknown

Unknown

Reduced for etesevimab

Unknown

N439K

Unknown

Unknown

Unknown

Reduced for imdevimab

Unknown

K444N, K444Q

Unknown

Unknown

Unknown

Reduced for imdevimab

Unknown

K444T

Unknown

Unknown

Unknown

Reduced for casirivimab + imdevimab

Unknown

V445A

Unknown

Unknown

Unknown

Reduced for casirivimab + imdevimab

Unknown

G446V

Unknown

Unknown

Unknown

Reduced for imdevimab

Unknown

L452R

Increased

Unknown

Reduced

Reduced for bamlanivimab

Reduced

Y453F

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

L455F

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

N460K, N460S, N460T

Unknown

Unknown

Unknown

Reduced for etesevimab

Unknown

G476S

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

S477N

Increased

Unknown

Unknown

Unknown

Unknown

V483A

 

 

 

Reduced for bamlanivimab

 

E484K

Unknown

Unknown

Unknown

Reduced for bamlanivimab + etesivimab, casirivimab

Reduced

E484Q

Unknown

Unknown

Unknown

Reduced for bamlanivimab + etesivimab, casirivimab

Unknown

F486V

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

F490S

Unknown

Unknown

Unknown

Reduced for bamlanivimab

Unknown

Q493E, Q493K

Unknown

Unknown

Unknown

Reduced for casirivimab

Unknown

Q493R

Unknown

Unknown

Unknown

Reduced for bamlanivimab + etesivimab

Unknown

S494P

Unknown

Unknown

Unknown

Reduced for bamlanivimab, casirivimab

Unknown

N501Y

Increased

Increased

Reduced

Reduced for etesevimab

Unknown

D614G

Increased

Unknown

No effect

No effect

No effect

Q677H, Q677P

Increased

Unknown

Unknown

Unknown

Unknown


 *Based on in vitro (experimental) data only.

**This dual codon mutation also causes failure of certain molecular detection assays.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

The ability to amplify the severe acute respiratory syndrome coronavirus 2 (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%.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Lauring AS, Hodcroft EB: Genetic variants of SARS-CoV-2-what do they mean? JAMA. 2021 Feb 9;325(6):529-531. doi: 10.1001/jama.2020.27124

2. Walensky RP, Walke HT, Fauci AS: SARS-CoV-2 variants of concern in the United States-challenges and opportunities. JAMA. 2021 Feb 17;325(11):1037-1038. doi: 10.1001/jama.2021.2294

3. Centers for Disease Control and Prevention: SARS-CoV-2 variant classifications and definitions. Available at www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html

4. World Health Organization: Weekly epidemiological update on COVID-19 - 8 June 2021. Available at www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---8-june-2021

5. Scripps Research: SARS-CoV-2 (hCoV-19) Mutation Situation Reports. Available at https://outbreak.info/situation-reports

6. European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. ECDC; June 24, 2021. Accessed June 28, 2021. Available at www.ecdc.europa.eu/en/covid-19/variants-concern

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

This test utilizes the commercially available Ion AmpliSeq SARS-CoV-2 Research Panel, a next-generation sequencing assay based on a sequencing by synthesis method. The assay amplifies 237 sequences ranging from 125 to 275 base pairs in length covering 99% of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Clinical respiratory tract specimens undergo manual total nucleic acid extraction and purification using MagMAX Viral / Pathogen Nucleic Acid Isolation Kit. The eluate undergoes automated reverse-transcription-polymerase chain reaction of viral sequences, DNA library preparation (including enzymatic shearing, adapter ligation, purification, normalization), DNA template preparation, and sequencing on the automated Genexus integrated sequencer. No-template control and a positive SARS-CoV-2 control are included in each assay run for quality control purposes. Viral sequence data are assembled using the Iterative Refinement Meta-Assembler (IRMA) application (50% base substitution frequency threshold) to generate unamended plurality consensus sequences of SARS-CoV-2 for analysis with the latest versions of the web-based application tools: https://pangolin.cog-uk.io/ for SARS-CoV-2 lineage assignment; https://clades.nextstrain.org/ for viral clade assignment and phylogenetic analysis;  https://covdb.stanford.edu/sierra/sars2/by-sequences/ for codon mutation calling, in comparison to wild-type reference sequence of Wuhan-Hu-1, lineage B, clade 19A.(Package insert: Ion AmpliSeq SARS-CoV-2 Research Panel. Life Technologies Corporation; rev. B.0, publ. no. MAN0019278 10/08/2020)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

2 to 10 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

30 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

87999

LOINC® 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
Result LOINC Value Tooltip
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
CVNGS SARS-CoV-2 Specimen Source 31208-2
616432 RdRp codon mutations of interest 99314-7
CVNGR Patient Race 72826-1
616433 RdRp mutations of unknown significance 99314-7
CVNGS SARS-CoV-2 Specimen Source 31208-2
CVNGE Patient Ethnicity 69490-1
CVNGR Patient Race 72826-1
CVPOS Recent Positive PCR Result within 5 days? 86955-2
CVNGE Patient Ethnicity 69490-1
CVPOS Recent Positive PCR Result within 5 days? 86955-2

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports