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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 SNOMED 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. 1

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
*122554006Capillary blood specimen (specimen)Capillary blood specimen20080731
*119294007Dried blood specimen (specimen)Dried blood specimen20020131

168137004Gastric aspirate sample (specimen)Gastric aspirate sample20060131

258606004Lower respiratory sample (specimen)Lower respiratory sample20080731

258411007Nasopharyngeal aspirate (specimen)Nasopharyngeal aspirate20080731

258500001Nasopharyngeal swab (specimen)Nasopharyngeal swab20080731

258412000Oropharyngeal aspirate (specimen)Oropharyngeal aspirate20080731

418564007Pleural fluid specimen (specimen)Pleural fluid specimen20080731

119342007Saliva specimen (specimen)Saliva specimen20040731
*119364003Serum specimen (specimen)Serum specimen20050131

734427005Specimen from duodenum obtained by aspiration (specimen)Specimen from duodenum obtained by aspiration20180131

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

445297001Swab of internal nose (specimen)Swab of internal nose20100731
*871810001Swab specimen from nasal mid-turbinate (specimen)Mid-turbinate nasal swab20200731

461911000124106

Swab specimen from oropharynx (specimen)

Oropharyngeal swab

20200731

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
*258580003Whole blood sample (specimen)Whole blood sample20080731
  • 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 idFully Specified Nameen-US Preferred TermEffective Time
60170009Analysis of arterial blood gases and pH (procedure)Analysis of arterial blood gases and pH20020131
444077007Analysis using reverse transcriptase polymerase chain reaction technique (procedure)Analysis using reverse transcriptase PCR20100131
61911006Blood gases, venous measurement (procedure)Blood gases, venous measurement20020131
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
871562009Detection of Severe acute respiratory syndrome coronavirus 2 (observable entity)Detection of Severe acute respiratory syndrome coronavirus 220200731
871553007Detection of Severe acute respiratory syndrome coronavirus 2 antigen (observable entity)Detection of Severe acute respiratory syndrome coronavirus 2 antigen20200731
76978006Enzyme-linked immunosorbent assay (procedure)Enzyme-linked immunosorbent assay20080731
30662005Fluorescent immunoassay (procedure)Fluorescent immunoassay20020131
414464004Immunoassay method (procedure)Immunoassay method20050131
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
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

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 idFully Specified Nameen-US Preferred TermEffective Time
16332841000119106Computed tomography angiography of pulmonary artery with contrast (procedure)CT angiography of pulmonary artery with contrast20170131
169069000Computed tomography of chest (procedure)CT of chest20040731
399208008Plain chest X-ray (procedure)Plain chest X-ray20050131
88628008Ultrasonography of lung (procedure)Ultrasonography of lung20020131

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 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
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
1155866009Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 encoding spike protein (substance)SARS-CoV-2 mRNA encoding spike protein20210731
1119343008Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance)Severe acute respiratory syndrome coronavirus 2 mRNA20210131
1240411000000107Ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance)Severe acute respiratory syndrome coronavirus 2 RNA20200731
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 idFully Specified Nameen-US Preferred TermEffective Time
260373001Detected (qualifier value)Detected20020131
419984006Inconclusive (qualifier value)Inconclusive20060131
260415000Not detected (qualifier value)Not detected20020131
895231008Not detected in pooled specimen (qualifier value)Not detected in pooled specimen20200731
897035006Severe acute respiratory syndrome coronavirus 2 antibody test negative (finding)SARS-CoV-2 antibody test negative20210131
897034005Severe acute respiratory syndrome coronavirus 2 antibody test positive (finding)SARS-CoV-2 antibody test positive20210131
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
125154007Specimen unsatisfactory for evaluation (finding)Specimen unsatisfactory for evaluation20020131

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. 

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



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