Guidance for mapping to SARS-CoV-2 LOINC terms

Synonyms: SARS-CoV-2, 2019 Novel Coronavirus, 2019-nCoV

The Regenstrief LOINC team has been working closely with APHL, CDC, FDA, labs, IVD manufacturers, and other stakeholders on codes specifically related to SARS-CoV-2/COVID-19. This work will help support the HHS COVID-19 Pandemic Response, Laboratory Data Reporting: CARES Act Section 18115 requirements.

IMPORTANT RECOMMENDATION

Regardless of the LOINC code you use, we strongly recommend that you report details about the specimen and the test kit along with the primary result.

Specimen details would ideally be reported using the HL7 SPM segment if using v2.5.1 or higher, OBR-15 if using v2.3.x, or the FHIR Specimen resource. If none of these are supported, specimen details can be sent as a separate observation result using LOINC 66746-9 Specimen type.

The test kit name and/or unique identifier would ideally be reported in OBX-17 and OBX-18, respectively. If this is not an option, test kit details can be sent as separate observation results using LOINC 67099-2 Vendor device name and/or 74711-3 Unique device identifier.

LOINCs for commercial in vitro diagnostics (IVD) test kits

The assays listed here are ONLY the ones that manufacturers have given us permission to list in order to make it as easy as possible for LOINC users to find the appropriate codes for their tests. The full list of LOINC mappings to SARS-CoV-2 IVD assays and LDTs approved under FDA EUA is available in the LIVD file posted on the CDC website. This file is currently updated weekly.

If you are a manufacturer, do not see your test kit listed, and would like us to include your test kit and corresponding LOINC information in this table, please contact us.

Manufacturer & test kit Result LOINC(s) Manufacturer's notice and if provided, URL for more information
Abbott Alinity i SARS-CoV-2 IgG 94563-4 (SARS-CoV-2 IgG qualitative)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Abbott Alinity m SARS-CoV-2 assay 94500-6 (SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Abbott ARCHITECT™ SARS-CoV-2 IgG 94563-4 (SARS-CoV-2 IgG qualitative)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Abbott ID NOW™ COVID-19 94534-5 (SARS-CoV-2 RdRp gene result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Abbott RealTime SARS-CoV-2 assay for m2000 instrument 94500-6 (SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

BioFire® COVID-19 Test 94565-9 (overall SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

bioMerieux ARGENE®
SARS-COV-2 R-GENE®
PCR1 - Order LOINC 94531-1
94533-7 (SARS-CoV-2 N gene result)
94534-5 (SARS-CoV-2 RdRp gene result)
94500-6 (overall SARS-CoV-2 result)PCR2 - Order LOINC 94502-2 (same as result)
94502-2 (SARS-related CoV result)

The SARS-COV-2 R-GENE® product is available as separate references under the following statuses:

  • RUO (Product Reference – 423717)
  • FDA – EUA (Product Reference – 423735)
  • CE-IVD (Product Reference – 423720)

LOINC codes are provided as an help to laboratories, they are not intended to imply or suggest any unapproved indication for use. It is the responsibility of laboratories to review proposed SARS-CoV-2 associated LOINC codes and decide whether they want to use them as provided or if they want to choose other codes in the LOINC data base.

https://www.mybiomerieux.com/

bioMerieux VIDAS® SARS-COV-2 IgG 94563-4 (SARS-CoV-2 IgG qualitative)

VIDAS® SARS-COV-2 IgG product is available as separated references under the following RUO (product reference: 423834-02) and CE-IVD status (product reference: 423834).

LOINC codes are provided as an help to laboratories, they are not intended to imply or suggest any unapproved indication for use. It is the responsibility of laboratories to review proposed SARS-CoV-2 associated LOINC codes and decide whether they want to use them as provided or if they want to choose other codes in the LOINC data base.

https://www.mybiomerieux.com/

bioMerieux VIDAS® SARS-COV-2 IgM 94564-2 (SARS-CoV-2 IgM qualitative)

VIDAS® SARS-COV-2 IgM product is available as separated references under the following RUO (product reference: 423833-02) and CE-IVD status (product reference: 423833).

LOINC codes are provided as an help to laboratories, they are not intended to imply or suggest any unapproved indication for use. It is the responsibility of laboratories to review proposed SARS-CoV-2 associated LOINC codes and decide whether they want to use them as provided or if they want to choose other codes in the LOINC data base.

https://www.mybiomerieux.com/

Bio-Rad Laboratories Platelia SARS-CoV-2 Total Antibody (IgA, IgM, IgG) Assay 94762-2 (SARS-CoV-2 Total Ab qualitative)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

www.bio-rad.com

Cepheid Xpert® Xpress SARS-CoV-2 94500-6 (SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

DiaSorin LIAISON® SARS-CoV-2 S1/S2 IgG 94563-4 (SARS-CoV-2 IgG qualitative)

Emergency Use Authorization

  • This test has not been FDA cleared or approved;
  • This test has been authorized by FDA under an EUA for use by authorized laboratories;
  • This test has been authorized only for the detection of IgG antibodies against SARS-CoV-2, not for any other viruses or pathogens; and
  • This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.

http://www.molecular.diasorin.com

DiaSorin Molecular Simplexa™ COVID-19 Direct 94500-6 (overall SARS-CoV-2 result)

Emergency Use Authorization

  • This test has not been FDA cleared or approved;
  • This test has been authorized by FDA under an EUA for use by authorized laboratories;
  • This test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens; and
  • This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.

http://www.molecular.diasorin.com

GenMark Dx ePlex® SARS-CoV-2 Test 94760-6 (SARS-CoV-2 N gene result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

https://www.genmarkdx.com/solutions/panels/eplex-panels/eplex-sars-cov-2-test/

Hologic Panther Fusion® SARS-CoV-2 94559-2 (SARS-CoV-2 ORF1ab region result)

The Panther Fusion® SARS-CoV-2 assay:

  • This test has not been FDA cleared or approved;
  • This test has been authorized by FDA under an EUA for use by authorized laboratories;
  • This test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens; and
  • This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.
Luminex ARIES SARS-CoV-2 Assay 94759-8 (SARS-CoV-2 overall result)

Emergency Use Authorization

The final decision regarding appropriate code(s) is the responsibility of the testing laboratory.

Luminex NxTAG CoV 94759-8 (SARS-CoV-2 overall result)

Emergency Use Authorization

The final decision regarding appropriate code(s) is the responsibility of the testing laboratory.

Quidel Lyra® SARS-CoV-2 Assay 94559-2 (SARS-CoV-2 ORF1ab region result)

Emergency Use Authorization

The final decision regarding appropriate code(s) is the responsibility of the testing laboratory.

Quidel Sofia 2 SARS Antigen FIA 95209-3 (SARS-CoV+SARS-CoV-2 Ag)

Emergency Use Authorization

The final decision regarding appropriate code(s) is the responsibility of the testing laboratory.

https://www.quidel.com/immunoassays/rapid-sars-tests/sofia-2-sars-antigen-fia

Roche cobas® SARS-CoV-2 94500-6 (overall SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Roche Elecsys Anti-SARS-CoV-2 94762-2 (SARS-CoV-2 Ab qualitative)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

Thermo Fisher Scientific TaqPath™ COVID-19 Combo Kit 94500-6 (overall SARS-CoV-2 result)

Emergency Use Authorization

The final decision regarding the appropriate code(s) is the responsibility of the testing laboratory.

https://www.thermofisher.com/covid19

Help with choosing the right LOINC

If you are using a commercial test kit that is not listed in the table above, we strongly recommend that you find out which test kit your laboratory is using and contact the manufacturer to determine which codes are most appropriate.

If you have no way of contacting the manufacturer, following are a few key recommendations:

  1. Choose the most specific code possible based on the test information, but do not overspecify. For example, if you are only testing nasopharyngeal specimens, use a LOINC term with System Nph.
  2. If you are testing upper or lower respiratory specimens (e.g., nasopharyngeal swabs, bronchoalveolar lavage, sputum), you should use the LOINC codes with System Respiratory to report SARS-CoV-2 testing results.
    • 94500-6 SARS coronavirus 2 RNA [Presence] in Respiratory specimen by NAA with probe detection is the most appropriate code if: 1) the gene or region being tested is not specified and you are reporting a qualitative result (e.g., Detected/Not detected); OR 2) you are reporting a single qualitative overall result based on a combination of individual test results.
  3. Panel LOINC codes should NOT be used for result reporting. Panel codes are used to order a battery of tests, not a single test.
  4. If your lab is running a single test, the same non-panel LOINC can be used to order and result the test.

The following tables contain detailed information about specific tests, specimens, and reporting, and the appropriate LOINC code to use for each.

Tests looking for SARS-CoV-2 nucleic acids (RNA)

Method: Sequencing

  Analyte LOINC number (type of result)
Saliva
  SARS-CoV-2 RNA 94822-4 (qualitative)

Method: Nucleic acid amplification with non-probe-based detection, such as melt curve analysis

  Analyte LOINC number (type of result)
Nasopharyngeal specimen
  SARS-CoV-2 RNA 94565-9 (qualitative)

Method: Nucleic acid amplification with probe-based detection

  Analyte LOINC number (type of result)
Saliva
  SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 94845-5 (qualitative)
Nasopharyngeal specimen
  SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 94759-8 (qualitative)
  SARS-CoV-2 N gene 94760-6 (qualitative)
ANY respiratory specimen (e.g., nasopharyngeal swabs, bronchoalveolar lavage, sputum)
  SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 94500-6 (qualitative)
  SARS-CoV-2 N gene 94533-7 (qualitative)
  SARS-CoV-2 E gene 94758-0 (qualitative)
  SARS-CoV-2 RdRp gene 94534-5 (qualitative)
    94646-7 (quantitative)
  SARS-CoV-2 ORF1ab region 94559-2 (qualitative)
    94644-2 (quantitative)
  SARS-CoV-2 S gene 94640-0 (qualitative)
    94642-6 (quantitative)
  SARS-related CoV* + MERS 94532-9 (qualitative)
  SARS-related CoV* 94502-2 (qualitative)
Serum or plasma
  SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 94660-8 (qualitative)
  SARS-CoV-2 E gene 94765-5 (qualitative)
  SARS-CoV-2 N gene 94766-3 (qualitative)
  SARS-CoV-2 S gene 94767-1 (qualitative)

Unspecified specimen

(i.e., unknown, or multiple unique specimen types may be tested and the specific type is reported separately)

  SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 94309-2 (qualitative)
    94819-0 (viral load in log copies/mL)
  SARS-CoV-2 N gene 94316-7 (qualitative)
    94510-5 (quantitative)
  SARS-CoV-2 N gene, CDC primer-probe set N1 94307-6 (qualitative)
    94311-8 (quantitative)
  SARS-CoV-2 N gene, CDC primer-probe set N2 94308-4 (qualitative)
    94312-6 (quantitative)
  SARS-CoV-2 E gene 94315-9 (qualitative)
    94509-7 (quantitative)
  SARS-CoV-2 RdRp gene 94314-2 (qualitative)
    94645-9 (quantitative)
  SARS-CoV-2 ORF1ab region 94639-2 (qualitative)
    94511-3 (quantitative)
  SARS-CoV-2 S gene 94641-8 (qualitative)
    94643-4 (quantitative)
  SARS-related CoV* 94647-5 (qualitative)
  SARS-like CoV N gene** 94310-0 (qualitative)
    94313-4 (quantitative)

 

*SARS-related CoV was previously represented as SARS-CoV + SARS-CoV-2 + SARS-like CoV. See the second question in the FAQ for more details about the nomenclature.
**This term was created based on an early version of the U.S. CDC kit that included a test for SARS-like CoV N gene. This test is no longer part of the CDC kit. We are trying to determine whether this analyte was really meant to be SARS-related CoV and will update the term depending on what we learn.

Test to determine the SARS-CoV-2 sequence

Method: Sequencing

  Isolate
SARS-CoV-2 whole genome 94764-8 (qualitative)

 

Test looking for SARS-CoV-2 antigen

Method: Rapid immunoassay (results in 60 minutes or less)

  Respiratory specimen (e.g., nasopharyngeal swabs, bronchoalveolar lavage, sputum)
SARS-CoV-2 Ag 94558-4 (qualitative)

 

Test looking for growth of SARS-CoV-2

Method: Organism specific culture

  Unspecified specimen
(i.e., unknown, or multiple unique specimen types may be tested and the specific type is reported separately)
SARS-CoV-2 94763-0 (qualitative)

 

Tests looking for antibodies to SARS-CoV-2

Method: Rapid immunoassay (results in 60 minutes or less)

  Serum or Plasma
SARS-CoV-2 IgA 94768-9 (qualitative)
SARS-CoV-2 IgG 94507-1 (qualitative)
SARS-CoV-2 IgM 94508-9 (qualitative)

Method: Immunoassay

  Serum or Plasma
SARS-CoV-2 antibody (non-specific) 94762-2 (qualitative)
  94769-7 (quantitative)
SARS-CoV-2 IgA 94562-6 (qualitative)
  94720-0 (quantitative)
SARS-CoV-2 IgG 94563-4 (qualitative)
  94505-5 (quantitative)
SARS-CoV-2 IgM 94564-2 (qualitative)
  94506-3 (quantitative)
SARS-CoV-2 IgG + IgM  (does NOT distinguish between the two) 94547-7 (qualitative)
SARS-CoV-2 antibody interpretation 94661-6 (qualitative interpretation, e.g., recent infection or past infection)

 

Frequently Asked Questions (FAQ)

What is the difference between SARS Coronavirus 2 (SARS-CoV-2) and COVID-19?

SARS-CoV-2 is the name of the virus that causes the COVID-19 disease. COVID-19 stands for Coronavirus Disease 2019. The LOINC Component represents the analyte being tested for, which is why the Components include “SARS Coronavirus 2” rather than “COVID-19”.

What is the difference between SARS coronavirus, SARS coronavirus 2, SARS-related coronavirus, and SARS-like coronavirus?

  • SARS-related coronavirus (SARS-related CoV) is a species of coronavirus in the sub-genus Sarbecovirus. SARS-related CoV includes SARS coronavirus (SARS-CoV), SARS coronavirus 2 (SARS-CoV-2), and bat SARS coronaviruses.
  • SARS-CoV is the specific virus responsible for Severe Acute Respiratory Syndrome, which was identified in 2003.
  • SARS-CoV-2 is the virus responsible for COVID-19. It was previously known as 2019 Novel coronavirus (2019-nCov).
  • Our current understanding of “SARS-like coronavirus” (SARS-like CoV) is that it is a group of viruses that are genetically similar to SARS-CoV but that the group does not include SARS-CoV or SARS-CoV-2. In other words, SARS-related CoV = SARS-CoV + SARS-CoV-2 + SARS-like CoV.

What are LOINC panel codes used for?

Panel codes should ONLY be used for test orders (batteries) and NOT for reporting results.

Panel codes have the word "panel" in the Component and a dash ("-") for the Property. They contain a collection of LOINC codes that are used to report the results for each individual test.

The current panel codes focused on SARS-CoV-2 testing include:

  • RT-PCR tests
    • LOINC 94531-1 (respiratory specimens)
    • LOINC 94306-8 (unspecified specimens)
  • IgG and IgM antibody (serology) tests

What is the difference between LOINC terms with System XXX and Respiratory?

Most testing for SARS-CoV-2 nucleic acids is currently being done on respiratory specimens, such as nasopharyngeal or throat swabs, or sputum. LOINC terms with System Respiratory are meant for tests done on respiratory specimens. If your lab is testing respiratory specimens, we strongly recommend that you use respiratory-specific LOINC codes.

Terms with System XXX are used when the specimen is unspecified, meaning that it is not known, or that multiple unique specimen types (e.g., respiratory, blood, urine, environmental) may be tested and the specimen information is sent separately in the electronic result message. For COVID-19 testing, LOINC terms with System XXX were created for the latter case where  respiratory, stool, urine, or blood, may be tested. However, most assays as of April 2, 2020 are only testing respiratory specimens, in which case the respiratory-specific LOINC codes are recommended.

Which LOINC codes should I use for the U.S. CDC RT-PCR test?

The U.S. CDC test kit, which is named “Centers for Disease Control and Prevention (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel”, corresponds to LOINC 94306-8 SARS Coronavirus 2 RNA panel - Unspecified specimen by NAA with probe detection. This panel code should NOT be used to report results.

For specific information about which codes to use to order and report results for the U.S. CDC RT-PCR test, please see the Association of Public Health Laboratories’ (APHL) website.

Why do all of the SARS-CoV-2 LOINC terms have specific methods?

In general, for common tests, we have methodless codes as well as codes with specific Methods. However, we are still in the early stages of learning about this virus, and we need to gather as much information as possible, so knowing the specific analyte that was tested and the methods that were used is important for tracking the virus, learning about the disease, and finding out which test targets and methods are the most accurate.

How can I download the Special Use prerelease terms?

We have collected SARS-CoV-2 and COVID-19 related terms on a dedicated page. You can sort and filter these lists of both published and pre-release terms. Once you have signed in to the website, you can export the data to a CSV file. As always, be aware that pre-release terms may change and additional codes may be added. It is imperative for you to keep track of updates.

How to contact us

If you have a question or issue regarding SARS-CoV-2 that is not addressed here or on our Prerelease page, please use our special contact us form.