Laboratory testing for COVID-19 and the associated SARS-CoV-2 virus includes methods that detect the presence of the virus and antibodies produced in response to infection, in specimen samples taken from potentially infected individuals. Test and investigation data which can be recorded using SNOMED CT includes:
- Specimen
- Laboratory Tests
- Radiology Procedures
- Substances and Virus
- Laboratory Test Results
- Other Investigations
These data elements are described below, with example SNOMED CT subsets for each.
2.4.1 Specimen
Specimens are samples of substances taken from an individual for testing - for example 258500001 | Nasopharyngeal swab (specimen)| or 119339001 | Stool specimen (specimen)| . The following specimens may be relevant to COVID-19 testing in one or more countries affected by the virus. 1
| CV19-INV-Specimen | ||||
|---|---|---|---|---|
| Concept id | Fully Specified Name | en-US Preferred Term | Effective Time | |
* | 697989009 | Anterior nares swab (specimen) | Anterior nares swab | 20140131 |
| 119297000 | Blood specimen (specimen) | Blood specimen | 20040731 | |
| * | 258607008 | Bronchoalveolar lavage fluid sample (specimen) | Bronchoalveolar lavage fluid sample | 20080731 |
| * | 122554006 | Capillary blood specimen (specimen) | Capillary blood specimen | 20080731 |
| * | 119294007 | Dried blood specimen (specimen) | Dried blood specimen | 20020131 |
| 168137004 | Gastric aspirate sample (specimen) | Gastric aspirate sample | 20060131 | |
| 258606004 | Lower respiratory sample (specimen) | Lower respiratory sample | 20080731 | |
| 258411007 | Nasopharyngeal aspirate (specimen) | Nasopharyngeal aspirate | 20080731 | |
| 258500001 | Nasopharyngeal swab (specimen) | Nasopharyngeal swab | 20080731 | |
| 258412000 | Oropharyngeal aspirate (specimen) | Oropharyngeal aspirate | 20080731 | |
| 418564007 | Pleural fluid specimen (specimen) | Pleural fluid specimen | 20080731 | |
| 119342007 | Saliva specimen (specimen) | Saliva specimen | 20040731 | |
| * | 119364003 | Serum specimen (specimen) | Serum specimen | 20050131 |
| 734427005 | Specimen from duodenum obtained by aspiration (specimen) | Specimen from duodenum obtained by aspiration | 20180131 | |
| 122610009 | Specimen from lung obtained by biopsy (specimen) | Specimen from lung obtained by biopsy | 20080731 | |
| 445447003 | Specimen from trachea obtained by aspiration (specimen) | Specimen from trachea obtained by aspiration | 20100731 | |
| 119334006 | Sputum specimen (specimen) | Sputum specimen | 20080731 | |
| 119339001 | Stool specimen (specimen) | Stool specimen | 20030731 | |
| * | 472901003 | Swab from nasal sinus (specimen) | Swab from nasal sinus | 20130131 |
| 445297001 | Swab of internal nose (specimen) | Swab of internal nose | 20100731 | |
| * | 871810001 | Swab specimen from nasal mid-turbinate (specimen) | Mid-turbinate nasal swab | 20200731 |
461911000124106 | Swab specimen from oropharynx (specimen) | Oropharyngeal swab | 20200731 | |
| 258529004 | Throat swab (specimen) | Throat swab | 20080731 | |
| 122877000 | Upper respiratory fluid specimen obtained by tracheal aspiration (specimen) | Upper respiratory fluid specimen obtained by tracheal aspiration | 20040731 | |
| 309164002 | Upper respiratory swab sample (specimen) | Upper respiratory swab sample | 20080731 | |
| 122575003 | Urine specimen (specimen) | Urine specimen | 20080731 | |
| * | 258580003 | Whole blood sample (specimen) | Whole blood sample | 20080731 |
- The specimens prefixed with a star '*' are a subtype of another member of this subset.
2.4.2 Laboratory Tests
Laboratory tests can be performed to detect the presence of the COVID-19 virus and antibodies produced in response to this virus. The following SNOMED CT concepts can be used to record laboratory tests that may be performed during the investigation process. 2
| CV19-INV-LaboratoryTests | |||
|---|---|---|---|
| Concept id | Fully Specified Name | en-US Preferred Term | Effective Time |
| 60170009 | Analysis of arterial blood gases and pH (procedure) | Analysis of arterial blood gases and pH | 20020131 |
| 444077007 | Analysis using reverse transcriptase polymerase chain reaction technique (procedure) | Analysis using reverse transcriptase PCR | 20100131 |
| 61911006 | Blood gases, venous measurement (procedure) | Blood gases, venous measurement | 20020131 |
| 871555000 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 | 20200731 |
| 871559006 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in bronchoalveolar lavage fluid (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in bronchoalveolar lavage fluid | 20200731 |
| 871556004 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in nasopharyngeal swab (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in nasopharyngeal swab | 20200731 |
| 871557008 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in oropharyngeal swab (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in oropharyngeal swab | 20200731 |
| 871558003 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in sputum (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 in sputum | 20200731 |
| 871560001 | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction (observable entity) | Detection of ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction | 20200731 |
| 871562009 | Detection of Severe acute respiratory syndrome coronavirus 2 (observable entity) | Detection of Severe acute respiratory syndrome coronavirus 2 | 20200731 |
| 871553007 | Detection of Severe acute respiratory syndrome coronavirus 2 antigen (observable entity) | Detection of Severe acute respiratory syndrome coronavirus 2 antigen | 20200731 |
| 76978006 | Enzyme-linked immunosorbent assay (procedure) | Enzyme-linked immunosorbent assay | 20080731 |
| 30662005 | Fluorescent immunoassay (procedure) | Fluorescent immunoassay | 20020131 |
| 414464004 | Immunoassay method (procedure) | Immunoassay method | 20050131 |
| 1240461000000109 | Measurement of severe acute respiratory syndrome coronavirus 2 antibody (observable entity) | Measurement of severe acute respiratory syndrome coronavirus 2 antibody | 20200731 |
| 1240471000000102 | Measurement of severe acute respiratory syndrome coronavirus 2 antigen (observable entity) | Measurement of severe acute respiratory syndrome coronavirus 2 antigen | 20200731 |
| 122435008 | Measurement of viral antibody (procedure) | Measurement of viral antibody | 20100131 |
| 9718006 | Polymerase chain reaction analysis (procedure) | Polymerase chain reaction analysis | 20080731 |
| 122433001 | Viral antigen assay (procedure) | Viral antigen assay | 20050131 |
| 118147004 | Viral nucleic acid assay (procedure) | Viral nucleic acid assay | 20020131 |
| 88667002 | Viral serologic study (procedure) | Viral serologic study | 20150131 |
2.4.3 Radiology Procedures
Radiology procedures are procedures that obtain images of the inside of the body. The following SNOMED CT concepts may be used to record radiology procedures that may be performed during the investigation and treatment of suspected or confirmed Covid-19 patients.
| CV19-INV-RadiologyProcedures | |||
|---|---|---|---|
| Concept id | Fully Specified Name | en-US Preferred Term | Effective Time |
| 16332841000119106 | Computed tomography angiography of pulmonary artery with contrast (procedure) | CT angiography of pulmonary artery with contrast | 20170131 |
| 169069000 | Computed tomography of chest (procedure) | CT of chest | 20040731 |
| 399208008 | Plain chest X-ray (procedure) | Plain chest X-ray | 20050131 |
| 88628008 | Ultrasonography of lung (procedure) | Ultrasonography of lung | 20020131 |
2.4.4 Substances and Virus
An antibody is a protective protein produced by the immune system in response to the presence of a foreign substance, called an antigen. The following antibody/antigen and virus organism concepts can be used to record the focus of a COVID-19 investigation.
| CV19-INV-SubstancesAndVirus | |||
|---|---|---|---|
| Concept id | Fully Specified Name | en-US Preferred Term | Effective Time |
| 840535000 | Antibody to severe acute respiratory syndrome coronavirus 2 (substance) | Antibody to SARS-CoV-2 | 20200131 |
| 840536004 | Antigen of severe acute respiratory syndrome coronavirus 2 (substance) | Antigen of SARS-CoV-2 | 20200131 |
| 870361009 | Immunoglobulin G antibody to Severe acute respiratory syndrome coronavirus 2 (substance) | SARS-CoV-2 IgG | 20200731 |
| 870362002 | Immunoglobulin M antibody to Severe acute respiratory syndrome coronavirus 2 (substance) | SARS-CoV-2 IgM | 20200731 |
| 1155866009 | Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 encoding spike protein (substance) | SARS-CoV-2 mRNA encoding spike protein | 20210731 |
| 1119343008 | Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance) | Severe acute respiratory syndrome coronavirus 2 mRNA | 20210131 |
| 1240411000000107 | Ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance) | Severe acute respiratory syndrome coronavirus 2 RNA | 20200731 |
| 840533007 | Severe acute respiratory syndrome coronavirus 2 (organism) | SARS-CoV-2 | 20200131 |
2.4.5 Laboratory Test Results
Laboratory test results are used to specify whether the Laboratory test focus was detected or not detected following the conducted laboratory test. The following qualifier values may be used for this purpose.
| CV19-INV-LabTestResults | |||
|---|---|---|---|
| Concept id | Fully Specified Name | en-US Preferred Term | Effective Time |
| 260373001 | Detected (qualifier value) | Detected | 20020131 |
| 419984006 | Inconclusive (qualifier value) | Inconclusive | 20060131 |
| 260415000 | Not detected (qualifier value) | Not detected | 20020131 |
| 895231008 | Not detected in pooled specimen (qualifier value) | Not detected in pooled specimen | 20200731 |
| 897035006 | Severe acute respiratory syndrome coronavirus 2 antibody test negative (finding) | SARS-CoV-2 antibody test negative | 20210131 |
| 897034005 | Severe acute respiratory syndrome coronavirus 2 antibody test positive (finding) | SARS-CoV-2 antibody test positive | 20210131 |
| 1240581000000104 | Severe acute respiratory syndrome coronavirus 2 detected (finding) | Severe acute respiratory syndrome coronavirus 2 detected | 20200731 |
| 1240591000000102 | Severe acute respiratory syndrome coronavirus 2 not detected (finding) | Severe acute respiratory syndrome coronavirus 2 not detected | 20200731 |
| 125154007 | Specimen unsatisfactory for evaluation (finding) | Specimen unsatisfactory for evaluation | 20020131 |
2.4.6 Other Investigations
Other investigative procedures - e.g. 719410009 | Consultation via video conference (procedure)| and 386472008 | Telephone consultation (procedure)| and 243791004 | Viral screening (procedure)| and 29303009 | Electrocardiographic procedure (procedure)| - may be performed to assess a COVID-19 patient. The following subset represents procedures that can be performed during the clinical assessment process.
| CV19-INV-InvestigationProcedures | |||
|---|---|---|---|
Intensional Definition: |
The following subset represents a collection of findings with context that may be related to these investigations and captured using SNOMED CT - for example 269944001 | Nasal swab taken (situation)| or 168331006 | Blood sent for virology (situation)| .
| CV19-INV-InvestigationFindings | |||
|---|---|---|---|
Intensional Definition: |
Footnotes
LOINC In Vitro Diagnostic (LIVD) Test Code Mapping for SARS-CoV-2 Tests, Division of Laboratory Systems, CDC, US
Why We Need Antigen and Antibody Tests for COVID-19, The Native Antigen Company, UK
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