Clinical labs are required by law to report all SARS-CoV-2 assay results. Two terminologies, Logical Observation Identifiers, Names, and Codes (LOINC) and Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT - SCT), assist with proper electronic computerized identification of the testing and patient results. To navigate this complicated task, Pam Banning, MLS(ASCP), PMP(PMI), and Andrea Pitkus, PhD, MLS(ASCP)CM, two members of the Laboratory LOINC Committee, offer some critical advice on coding and related tools and resources, and address some of the challenges labs are facing with LOINC and SNOMED CT encoding of lab results for COVID-19 testing.

“Standardized terminology codes enable diagnostic analytics to take place on incoming data from a variety of sources. This is critical for accurate interpretation of population health,” said Banning, senior content developer at 3M HIS/Healthcare Data Dictionary and co-chair of the Laboratory LOINC Committee. This is a communication effort between  labs and their information technology departments, or wherever laboratory information system (LIS) database administration takes place, she noted.

LOINC is an international vocabulary standard system for identifying clinical information in electronic records. It identifies lab assays, clinical observations, and survey assessments through six attributes: component, property, timing, system, scale, and method. The attributes “roll up” into a numeric tag that all computer systems having the database resource recognize and utilize. SNOMED CT is a global system for clinical terminology in electronic health records.

LOINC distinguishes the different ways COVID-19 testing is performed, according to Pitkus, clinical terminology domain expert with the Problem Concept Maps Consortium at the University of Wisconsin School of Medicine and Public Health. SNOMED CT encodes specimen types and specimen sources as well as qualitative result values. “If codes are missing or incorrect, manual processing of lab data needs to be performed, which can delay responses, decisions, and impact quality and safety of patient care whether on an individual or population level,” Pitkus noted.

COVID-19 is reportable by state law but is also considered a Nationally Notifiable Condition. Electronic Lab Reporting (ELR) requires these codes from the performing laboratory, and in some jurisdictions from the ordering laboratory, if testing has been sent to a reference lab, said Pitkus. LOINC codes are also part of the specifications for electronic case reporting that providers use to notify the Centers for Disease Control and Prevention (CDC) about COVID-19 cases, she explained. LOINC and SNOMED CT aren’t used for reimbursement. However, some insurance companies require LOINC codes for all test results as part of their contracting process with laboratories. The Department of Health and Human Services on June 4 announced new laboratory data reporting guidance for COVID-19 testing.

Many clinical decision support tools within LIS and electronic health record (EHR) use LOINC and SNOMED CT. Apps on mobile devices or in patient- or consumer-facing portals as well as public health jurisdictions also employ LOINC and SNOMED CT to process lab data.

For this reason, clinical labs should ensure that LIS and EHR partners have up-to-date versions of LOINC and SNOMED CT mapped to their laboratory test data. “Many LIS vendors are supporting the LOINC pre-release COVID-19 codes, so folks don’t have to wait for the next LOINC release in June 2020,” said Pitkus. “SNOMED CT had several releases earlier this year including COVID-19 terms, such as those used to note the diagnosis of a patient with coronavirus.” 

SNOMED CT codes from the specimen hierarchy are useful in encoding specimen types. “Often this requires specimen terms to build in the appropriate LIS dictionary so the terms and codes correctly populate HL7 messages sent to providers and/or public health,” Pitkus said. Specimen sources indicate the location of collection, such as right ear, left leg, or upper left lobe of the lung such as from a bronchial wash or lavage specimen. “Sources are critical in public health reporting as some diseases are only reportable if they are detected in a sterile source like cerebrospinal fluid or urine,” she continued.

Issues have arisen in reporting of COVID-19-related data, the two experts acknowledged. SARS-CoV-2 results are reportable whether they’re positive or negative. However, sensitivity and specificity has been reported to be 30% lower in swabs collected from oral sources, compared with nasopharyngeal sources. Having the correct specimen identified in SNOMED CT can provide assurance of the value received or give a clinician pause due to a lower sensitivity collection. “These details matter to public health, as patients with a false negative result may infect others instead of quarantining, especially if asymptomatic,” Pitkus said.

In a recent AACC Artery post, Pitkus asked colleagues what LOINC/SNOMED codes they were using for mapping specimen types and sources, as well as the methods for sending ELR messages, and what information labs were sending to public health departments. “One would hope Artery participants took the questions from her post, communicated with their IT department,” and resolved any issues, said Banning.

In reaching out with 3M’s free ongoing offer to assist in SARS-CoV-2 LOINC mapping, Banning’s team noticed that many labs weren’t aware of the standardized terminology, even though it has been in the industry for 25 years. “A short education communication helped most understand it, but it took the use case of a pandemic to get the needed attention and priority,” she said. “There is a tsunami of COVID19 data being collected, and the analytics for years to come will perform best on identified types of data.”

To assist labs, CDC recently posted an updated version of the LOINC In Vitro Diagnostic Test Code Mapping Tool for SARS-CoV-2 Test Results. The tool provides laboratories with additional guidance as to the correct LOINC and SNOMED CT codes for their test results and specimen collection information by vendor kit or method, including analyzers. CDC has a wealth of regularly updated laboratory resources on its website. Banning cautions that labs build their LIS compendium in the same format  as the attributes suggested by the test vendor before adopting any guidance from CDC’s website. If an assay is intended to be qualitative, the LIS should contain a qualitative format; the same is true for quantitation values and for sequencing terms.

Choosing the correct term for assays is critical, Banning said. Additionally, any change of test or result name, units of measure, or report format may impact the LOINC a lab chooses. “Then it is time for a quick audit to assure the current data is tagged correctly,” she said.

Laboratories should also check with each public health jurisdiction for ELR reportable criteria as they might be slightly different, advised Pitkus. “Ideally all labs should report in HL7 version 2.51 to help promote interoperability. They will want to ensure they are sending the specimen type, specimen source, and correct SNOMED CT codes for each, along with the lab results and correct LOINC codes for them,” Pitkus said.

Many challenges remain with testing. As supply chain and laboratory testing capacity experience ups and downs, labs may switch test methods orderable in their systems or those sent out to public health labs or reference labs, Pitkus said. Some are even activating and inactivating orders for clinicians, depending on changing circumstances. Such circumstances require a quick LOINC check that the new process is encoded correctly.

Meeting public health reporting requirements on specimen type, specimen source, and patient demographics/contact information is another challenge. Labs will need to work with upstream specimen collection sites, including drive-through collection sites, to meet these requirements, Pitkus said. “Contributing to this challenge is receipt of paper requisitions and orders from some of these ordering and collecting locations. It creates a burden on laboratories which are already taxed,” she added.

Labs that devise laboratory-developed tests might find they don’t have a LOINC code that accurately matches their tests, specimens, or methods. For these cases, the lab should request a LOINC code, Pitkus suggested. “Such distinct codes will ensure their results are not commingled with other COVID test results that might have different sensitivities and specificities,” she said. Banning added that holds terms for saliva nucleic acid testing, as well as respiratory, antibody serologies, and more. The standard release is expected in June 2020.

Laboratory professionals are always welcome to join the LOINC committee and LOINC meetings, and contribute their expertise to helping ensure this laboratory standard meets laboratory needs. More information about LOINC and COVID-19 is available on AACC’s Lab Tests Online.