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 will help support the HHS COVID-19 Pandemic Response, Laboratory Data Reporting: CARES Act Section 18115 requirements that were published on June 4, 2020. Additional information regarding the June 4 requirements, including technical specifications, was published by HHS on July 31, 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 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 for the SARS-CoV-2 virus

 

1. SARS-CoV-2 nucleic acids (RNA)

Method: Sequencing

Analyte LOINC number (type of result)
Saliva
SARS-CoV-2 RNA 94822-4 (qualitative)
ANY respiratory specimen (e.g., nasopharyngeal swabs, bronchoalveolar lavage, sputum)
SARS-CoV-2 RNA 95424-8 (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)
SARS-CoV-2 N gene 95425-5 (qualitative)
Nasal specimen
SARS-CoV-2 RNA (specific gene not known OR reporting a single result based on a combination of tests) 95406-5 (qualitative)
SARS-CoV-2 N gene 95409-9 (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)
94745-7 (quantitative)
SARS-CoV-2 N gene 94533-7 (qualitative)
SARS-CoV-2 N gene, CDC primer-probe set N1 94756-4 (qualitative)
SARS-CoV-2 N gene, CDC primer-probe set N2 94757-2 (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)
SARS-related CoV* E gene 94758-0 (qualitative)
Influenza virus A & Influenza virus B & SARS-CoV-2 (distinguishes between all 3) 95423-0 (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 N gene 94766-3 (qualitative)
SARS-CoV-2 S gene 94767-1 (qualitative)
SARS-related CoV* E gene 94765-5 (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)
94746-5 (quantitative)
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 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-related CoV* E gene 94315-9 (qualitative)
94509-7 (quantitative)
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.


2. 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)
SARS-CoV+SARS-CoV-2 Ag 95209-3 (qualitative)

 


3. SARS-CoV-2 sequence

Method: Sequencing

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

4. 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 for antibodies to SARS-CoV-2

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

Serum, Plasma, or Blood
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 IgA+IgM (does NOT distinguish between the two) 95125-1 (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)
Dried blood spot
SARS-CoV-2 IgG 94761-4 (qualitative)
SARS-CoV-2 IgM 95416-4 (qualitative)

Method: Pseudovirus neutralization test (pVNT)

Serum
SARS-CoV-2 neutralizing antibody 95411-5 (qualitative)
95410-7 (titer)

 

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)
  • RT-PCR tests for SARS-CoV-2 and Influenza A & B
    • LOINC 95422-2 (respiratory specimens; SARS-CoV-2 N gene, Influenza A, Influenza B)
    • LOINC 95380-2 (respiratory specimens; SARS-CoV-2 RNA, SARS-related CoV, Influenza A, Influenza B)
  • 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 July 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.