Tests and Investigations

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.

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.

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.

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.

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

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

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

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

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: < 386053000 |Evaluation procedure (procedure)| OR < 308335008 |Patient encounter procedure (procedure)| OR < 17636008 |Specimen collection (procedure)|

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: < 313333008 |Sample obtained (situation)| OR < 168123008 |Sample sent for examination (situation)|

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Footnotes

1 LOINC In Vitro Diagnostic (LIVD) Test Code Mapping for SARS-CoV-2 Tests, Division of Laboratory Systems, CDC, US

2 Why We Need Antigen and Antibody Tests for COVID-19, The Native Antigen Company, UK