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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 SNOEMD CT includes:

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.

CV19-INV-Specimen
Concept idFully Specified Nameen-US Preferred TermEffective Time
697989009Anterior nares swab (specimen)Anterior nares swab20140131
119297000Blood specimen (specimen)Blood specimen20040731
258607008Bronchoalveolar lavage fluid sample (specimen)Bronchoalveolar lavage fluid sample20080731
258606004Lower respiratory sample (specimen)Lower respiratory sample20080731
258500001Nasopharyngeal swab (specimen)Nasopharyngeal swab20080731
258411007Nasopharyngeal aspirate (specimen)Nasopharyngeal aspirate20080731
258412000Oropharyngeal aspirate (specimen)Oropharyngeal aspirate20080731
418564007Pleural fluid specimen (specimen)Pleural fluid specimen20080731
122610009Specimen from lung obtained by biopsy (specimen)Specimen from lung obtained by biopsy20080731
445447003Specimen from trachea obtained by aspiration (specimen)Specimen from trachea obtained by aspiration20100731
119334006Sputum specimen (specimen)Sputum specimen20080731
119339001Stool specimen (specimen)Stool specimen20030731
472901003Swab from nasal sinus (specimen)Swab from nasal sinus20130131
258529004Throat swab (specimen)Throat swab20080731
122877000Upper respiratory fluid specimen obtained by tracheal aspiration (specimen)Upper respiratory fluid specimen obtained by tracheal aspiration20040731
309164002Upper respiratory swab sample (specimen)Upper respiratory swab sample20080731
122575003Urine specimen (specimen)Urine specimen20080731

461911000124106

Swab specimen from oropharynx (specimen)

Oropharyngeal swab

20200731

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.

CV19-INV-LaboratoryTests
Concept idFully Specified Nameen-US Preferred TermEffective Time
444077007Analysis using reverse transcriptase polymerase chain reaction technique (procedure)Analysis using reverse transcriptase PCR20100131
76978006Enzyme-linked immunosorbent assay (procedure)Enzyme-linked immunosorbent assay20080731
30662005Fluorescent immunoassay (procedure)Fluorescent immunoassay20020131
414464004Immunoassay method (procedure)Immunoassay method20050131
122435008Measurement of viral antibody (procedure)Measurement of viral antibody20100131
9718006Polymerase chain reaction analysis (procedure)Polymerase chain reaction analysis20080731
122433001Viral antigen assay (procedure)Viral antigen assay20050131
118147004Viral nucleic acid assay (procedure)Viral nucleic acid assay20020131
88667002Viral serologic study (procedure)Viral serologic study20150131
1445431000168101Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 (observable entity)Detection of nucleic acid of severe acute respiratory syndrome coronavirus 220200731
1454581000168100Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in bronchoalveolar lavage fluid (observable entity)Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in bronchoalveolar lavage fluid20200731
1454411000168105Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in nasopharyngeal swab (observable entity)Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in nasopharyngeal swab20200731
1454491000168101Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in oropharyngeal swab (observable entity)Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in oropharyngeal swab20200731
1454561000168109Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in sputum (observable entity)Detection of nucleic acid of severe acute respiratory syndrome coronavirus 2 in sputum20200731
1240511000000106Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction (observable entity)  Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction20200731
1240461000000109Measurement of severe acute respiratory syndrome coronavirus 2 antibody (observable entity)Measurement of severe acute respiratory syndrome coronavirus 2 antibody20200731
1240471000000102Measurement of severe acute respiratory syndrome coronavirus 2 antigen (observable entity)Measurement of severe acute respiratory syndrome coronavirus 2 antigen20200731

Please refer to 2.4.1 Extension Concepts - Tests and Procedures for a list of known extension concepts.

2.4.3 Substances and Virus 

Please refer to 2.4.1 Extension Concepts - Tests and Procedures for a list of known extension concepts. 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 idFully Specified Nameen-US Preferred TermEffective Time
840535000Antibody to severe acute respiratory syndrome coronavirus 2 (substance)Antibody to SARS-CoV-220200131
840536004Antigen of severe acute respiratory syndrome coronavirus 2 (substance)Antigen of SARS-CoV-220200131
840533007

Severe acute respiratory syndrome coronavirus 2 (organism)

SARS-CoV-2

20200131
870361009Immunoglobulin G antibody to severe acute respiratory syndrome coronavirus 2 (substance)SARS-CoV-2 IgG20200731
870362002Immunoglobulin M antibody to severe acute respiratory syndrome coronavirus 2 (substance)SARS-CoV-2 IgM20200731
1240411000000107Ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance)Severe acute respiratory syndrome coronavirus 2 RNA20200731

2.4.4 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 idFully Specified Nameen-US Preferred TermEffective Time
260373001Detected (qualifier value)Detected20020131
419984006Inconclusive (qualifier value)Inconclusive20060131
260415000Not detected (qualifier value)Not detected20020131
125154007Specimen unsatisfactory for evaluation (finding)Specimen unsatisfactory for evaluation20020131
1240581000000104Severe acute respiratory syndrome coronavirus 2 detected (finding)Severe acute respiratory syndrome coronavirus 2 detected20200731
1240591000000102Severe acute respiratory syndrome coronavirus 2 not detected (finding)Severe acute respiratory syndrome coronavirus 2 not detected20200731

Please refer to 2.4.1 Extension Concepts - Tests and Procedures for a list of known extension concepts.

2.4.5 Other Investigations 

Other investigative procedures - e.g. 719410009 | Consultation via video conference (procedure)|  and  386472008 | Telephone consultation (procedure)|  and  243791004 | Viral screening (procedure)| - may be performed to assess a COVID-19 patient. The following subset represents procedures that can be performed during the clinical assessment process. 

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

Please refer to 2.4.1 Extension Concepts - Tests and Procedures for a list of known extension concepts.



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