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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 severe acute respiratory syndrome coronavirus 2 (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 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


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.


Useful For

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

 

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, 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

Clinical Information

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

Not applicable

Interpretation

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:

 

WHO label

SARS-CoV-2 PANGO lineage

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

Alpha

B.1.1.7

No effect

Good

Good

Good

Good

Good

Beta

B.1.351

Increased

Reduced

Reduced(b)

Reduced

Reduced

Good

Gamma

P.1

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Delta

AY……(c)

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Delta

B.1.617.2

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Epsilon

B.1.427

Unknown

Reduced

Reduced(d)

Reduced

Reduced

Reduced

Epsilon

B.1.429

Unknown

Reduced

Reduced(d)

Reduced

Reduced

Reduced

Zeta

P.2

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Eta

B.1.525

Unknown

Reduced

Reduced(e)

Reduced

Reduced

Reduced

Theta

P.3

Unknown

Reduced

Reduced(b)

Unknown

Unknown

Unknown

Iota

B.1.526

Unknown

Reduced

Reduced(e)

Reduced

Reduced

Reduced

Kappa

B.1.617.1

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Lambda

C.37

Unknown

Unknown

Unknown

Unknown

Unknown

Unknown

Mu

B.1.621

Unknown

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Omicron

B.1.1.529

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

Omicron

BA……(c)

Increased

Reduced

Reduced(b)

Reduced

Reduced

Reduced

 

a. Based on in vitro (experimental) data only

b. Reduced efficacy of bamlanivimab, etesevimab, and casirivimab

c. All current Pango lineage designations that start with AY and BA are sublineages of the Delta and Omicron variants, respectively

d. Reduced efficacy of bamlanivimab

e. Reduced efficacy of bamlanivimab and casirivimab

 

Current antiviral drugs, such as remdesivir, that are used to treat COVID-19 are nucleoside analogs that inhibit viral RNA-dependent polymerase (RdRp) of coronaviruses (including SARS-CoV-2) and prevent viral replication. Genotypic mutations occurring alone or in combination in the RdRp-encoding region of the SARS-CoV-2 nsp12 gene have been reported to be associated with resistance to these antiviral drugs. The RdRp codon mutations associated with such antiviral resistance are: F480L, D484Y, and V557L.

 

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

Unknown

Unknown

Unknown

Reduced for bamlanivimab

Unknown

E484A

Unknown

Unknown

Reduced

Reduced excepted for sotrovimab

Reduced

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.

Clinical Reference

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

 

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

87999

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

Day(s) Performed

Varies

Report Available

2 to 10 days