SARS Coronavirus 2

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

LOINC Webinar regarding SARS-CoV-2/COVID-19

The recorded three-hour webinar is now available to be viewed.

More Info

Links related to SARS-CoV-2 and COVID-19

Frequently Asked Questions

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.

LOINCs for commercial in vitro diagnostics (IVD) test kits

The Regenstrief LOINC team has been working closely with a variety of IVD manufacturers to create and assign appropriate LOINC codes for their SARS-CoV-2 test kits. Some of these manufacturers have given us permission to list their test kits and corresponding LOINC codes on this page in order to make it as easy as possible for LOINC users to find the appropriate codes for their tests.

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 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)

SARS-COV-2 R-GENE® product is under the Research Use Only status. 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/

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.

GenMark Dx ePlex® SARS-CoV-2 Test 94533-7 (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 94500-6 (SARS-CoV-2 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.
Quidel Lyra® SARS-CoV-2 Assay 94559-2 (SARS-CoV-2 ORF1ab region result)

Emergency Use Only

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

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.

If the kit I'm using is not listed above, which LOINC codes should I use for test results?

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. If you are only testing respiratory specimens, 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.
  2. Panel LOINC codes should NOT be used for result reporting. Panel codes are used to order a battery of tests, not a single test.
  3. 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 the SARS-CoV-2 nucleic acids (RNA)

Method: Nucleic acid amplification with probe-based detection

  Respiratory specimen

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) 94500-6 (qualitative) 94309-2 (qualitative)
SARS-CoV-2 N gene 94533-7 (qualitative) 94316-7 (qualitative)
94307-6 (qualitative, CDC primer-probe set N1)
94308-4 (qualitative, CDC primer-probe set N2)
94510-5 (quantitative)
94311-8 (quantitative, CDC primer-probe set N1)
94312-6 (quantitative, CDC primer-probe set N2)
SARS-CoV-2 E gene   94315-9 (qualitative)
94509-7 (quantitative)
SARS-CoV-2 RdRp gene 94534-5 (qualitative) 94314-2 (qualitative)
SARS-CoV-2 ORF1ab region 94559-2 (qualitative) 94511-3 (quantitative)
SARS-related CoV* + MERS 94532-9 (qualitative)  
SARS-related CoV* 94502-2 (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. We plan to update the LOINC Components for these terms. 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.

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

  Nasopharyngeal specimen
SARS-CoV-2 RNA 94565-9 (qualitative)

Tests looking for SARS-CoV-2 antigen

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

  Respiratory specimen
SARS-CoV-2 Ag 94558-4 (qualitative)

Tests looking for antibodies to SARS-CoV-2

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

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

Method: Immunoassay

  Serum or Plasma
SARS-CoV-2 IgA 94562-6 (qualitative)
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)

 

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?

These Special Use terms are not yet part of an official LOINC release and therefore not available as a direct download from our website, nor are they available via our FHIR terminology services (API). It is important for us to maintain this distinction. You are able to copy/paste the data from the prerelease page for use in your system. Note that the Special Use terms may change and additional codes may be added. It is imperative for you to keep track of updates. The terms will be published in the next LOINC release (June).

 

Have a different question?

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