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 terminology specifically related to SARS-CoV-2/COVID-19. This work helps support the HHS COVID-19 Pandemic Response, Laboratory Data Reporting: CARES Act Section 18115 requirements that were published on June 4, 2020.

LOINCs for commercial in vitro diagnostics (IVD) and laboratory-developed tests (LDTs)

The full list of IVD assays and LDTs approved under FDA EUA and corresponding LOINC terms is available in the LIVD file posted on the CDC website. This file is maintained jointly by CDC, FDA, APHL, IVD manufacturers, and the Regenstrief LOINC team and is updated weekly. It currently contains LOINC order and result codes, SNOMED CT specimen and result codes, and device identifier information.

We previously published a list of LOINC codes corresponding to a subset of assays for which we had manufacturers' permission to do so on this page; we decided to remove that table and link to the full file published by the CDC in order to provide consistent information across assays and avoid confusion as to why only a subset was published on this page.

Help with choosing the right LOINC

If you are using a commercial test kit that is not listed in the LIVD file, we strongly recommend that you 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. Narrow down the potential LOINC matches based on the type of test. Molecular tests are represented by LOINC terms that include "RNA" or a specific gene in the Component; antibody tests contain "Ab"; and antigen tests contain "Ag".
  2. 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.
  3. 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.
  4. Panel LOINC codes should NOT be used for result reporting. Panel codes are used to order a battery of tests, not a single test.
  5. If your lab is running a single test, the same non-panel LOINC can be used to order and result the test.
  6. LOINC codes that include "Ab" without specifying the type of antibody (IgG, IgM, etc.) represent measurement of the total antibodies present, meaning the sum of IgA, IgG, and IgM. For tests that specifically measure IgG, IgM, or the combination of IgG and IgM, use terms that include "Ab.IgG", "Ab.IgM, or "Ab.IgG+IgM" in the Component, respectively.

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, and SARS-related 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).

What are LOINC panel codes used for?

Panel codes should ONLY be used for test orders (batteries) and NOT for reporting results. LOINC panels contain collections of LOINC codes, where each individual result is reported using one of the codes in the collection.

Panel codes have the word "panel" in the Component and a dash ("-") for the Property.

Note that non-panel LOINC codes can be used to both order and result single 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.

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.

What version should I use for pre-release terms?

Pre-released LOINC terms are those that are published in between official releases. If you need to include a version when you are using one of these codes, we recommend using the following: {Version of the upcoming LOINC release}-pre. For example, the June 2021 LOINC release will be release 2.70. The version of pre-release codes published between the 2.69 release in December 2020 and 2.70 is 2.70-pre.

Are there different LOINC codes for consumer-collected specimens or consumer-run tests?

We currently do not have separate LOINC codes for consumer testing, either for consumer-collected specimens or consumer-performed tests, because the defining aspects of the test (the analyte, specimen, property being measured, etc.) are the same as tests run in a laboratory or provider's office.

How do I report which variant of SARS-CoV-2 was identified?

For reporting the SARS-CoV-2 variant strain identified, various codes are available in LOINC depending on the nomenclature used. For the most general code (nomenclature unspecified), use LOINC: 96741-4 SARS-CoV-2 (COVID-19) variant [Type] in Specimen. To report the lineage for the variant, use LOINC: 96895-8 SARS-CoV-2 (COVID-19) lineage [Type] in Specimen. To report the clade for the variant, use LOINC: 96896-6 SARS-CoV-2 (COVID-19) clade [Type] in Specimen.

How do I report the SARS-CoV-2 mutation(s) identified?

To report the mutation(s) identified within the S (spike) gene of SARS coronavirus 2 (SARS-CoV-2) by molecular methods, use LOINC: 96751-3 SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular method. For reporting whether or not a known mutation was detected within the S (spike) gene, use LOINC: 96752-1 SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular method.

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.