SARS-CoV-2-RT-PCR


Parameter Case Report Form and Response Options

SARS-CoV-2-RT-PCR Detected Not detected Inconclusive
SARS-CoV-2 (COVID-19) RNA Presence in Respiratory specimen

This profile of a FHIR Observation is derived from the Laboratory Observation-profile of the Medical Informatics Initiative (MII). Further information and examples can be found in the MII's Implementation Guide.


Profile - SARS-CoV-2-RT-PCR

Canonical: https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr

Snapshot

useΣ ?!0..1codeBinding
systemS Σ1..1uriFixed Value
versionΣ0..1string
codeS Σ1..1codeFixed Value
displayΣ0..1string
userSelectedΣ0..1boolean
textΣ0..1string
systemS Σ1..1uri
valueS Σ1..1string
periodΣ I0..1Period
assignerS Σ I1..1MII-Reference(Organization)
basedOnΣ I0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
partOfΣ I0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)
statusS Σ ?!1..1codeBinding
loinc-observationS Σ1..1Coding
observation-categoryS Σ1..1Coding
textΣ0..1string
systemS Σ1..1uri
versionΣ0..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textΣ0..1string
subjectS Σ I1..1MII-Reference(Patient | Group)
focusΣ I0..*Reference(Resource)
encounterS Σ I0..1Reference(Encounter)
QuelleKlinischesBezugsdatumS I0..1Extension(Coding)
issuedS Σ0..1instant
performerΣ I0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)
systemS Σ1..1uri
versionΣ0..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textΣ0..1string
dataAbsentReasonS I0..1CodeableConceptBinding
interpretationS0..*CodeableConceptBinding
noteS0..*Annotation
bodySite0..0CodeableConcept
methodS0..1CodeableConcept
referenceS Σ I0..1string
typeΣ0..1uriBinding
identifierS Σ0..1Identifier
displayΣ0..1string
deviceS I0..1Reference(Device | DeviceMetric)
lowI0..1SimpleQuantity
highI0..1SimpleQuantity
type0..1CodeableConceptBinding
appliesTo0..*CodeableConcept
ageI0..1Range
text0..1string
hasMemberΣ I0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)
derivedFromΣ I0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)
codeΣ1..1CodeableConcept
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonI0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)


ValueSets

Valuesets are provided with SNOMED-CT codes.


Canonical: https://www.netzwerk-universitaetsmedizin.de/fhir/ValueSet/detected-not-detected-inconclusive

ValueSet 'DetectedNotDetectedInconclusive'

Version1.0.6
Published byBerlin Institute of Health at Charité (BIH)
StatusActive
ExperimentalFalse

A set of codes representing the result of a test as detected, not detected, or inconclusive.

Contact Information

Website: https://www.bihealth.org/en/re...

This value set includes codes from the following code systems:


Examples

SARS-CoV-2 test positive

{
    "resourceType": "Observation",
    "id": "sars-cov-2-rt-pcr-positive",
    "meta": {
        "profile":  [
            "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr"
        ]
    },
    "identifier":  [
        {
            "type": {
                "coding":  [
                    {
                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
                        "code": "OBI"
                    }
                ]
            },
            "system": "https://www.charite.de/fhir/CodeSystem/lab-identifiers",
            "value": "94500-6_SARS-CoV-2-RNA-Presence-in-Respiratory-specimen",
            "assigner": {
                "reference": "Organization/Charité"
            }
        }
    ],
    "category":  [
        {
            "coding":  [
                {
                    "system": "http://loinc.org",
                    "code": "26436-6"
                },
                {
                    "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                    "code": "laboratory"
                }
            ]
        }
    ],
    "code": {
        "coding":  [
            {
                "code": "94500-6",
                "system": "http://loinc.org",
                "display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection"
            }
        ],
        "text": "SARS-CoV-2-RNA (PCR)"
    },
    "status": "final",
    "subject": {
        "reference": "Patient/gecco-patient"
    },
    "effectiveDateTime": "2020-11-10T15:50:41+01:00",
    "valueCodeableConcept": {
        "coding":  [
            {
                "code": "260373001",
                "system": "http://snomed.info/sct",
                "display": "Detected (qualifier value)"
            }
        ],
        "text": "SARS-CoV-2-RNA positiv"
    }
}


SARS-CoV-2 test negative

{
    "resourceType": "Observation",
    "id": "sars-cov-2-rt-pcr-negative",
    "meta": {
        "profile":  [
            "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr"
        ]
    },
    "identifier":  [
        {
            "type": {
                "coding":  [
                    {
                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
                        "code": "OBI"
                    }
                ]
            },
            "system": "https://www.charite.de/fhir/CodeSystem/lab-identifiers",
            "value": "94500-6_SARS-CoV-2-RNA-Presence-in-Respiratory-specimen",
            "assigner": {
                "reference": "Organization/Charité"
            }
        }
    ],
    "category":  [
        {
            "coding":  [
                {
                    "system": "http://loinc.org",
                    "code": "26436-6"
                },
                {
                    "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                    "code": "laboratory"
                }
            ]
        }
    ],
    "code": {
        "coding":  [
            {
                "code": "94500-6",
                "system": "http://loinc.org",
                "display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection"
            }
        ],
        "text": "SARS-CoV-2-RNA (PCR)"
    },
    "status": "final",
    "subject": {
        "reference": "Patient/gecco-patient"
    },
    "effectiveDateTime": "2020-10-16T08:49:21+02:00",
    "valueCodeableConcept": {
        "coding":  [
            {
                "code": "260415000",
                "system": "http://snomed.info/sct",
                "display": "Not detected (qualifier value)"
            }
        ],
        "text": "SARS-CoV-2-RNA negativ"
    }
}


SARS-CoV-2 test inconclusive

{
    "resourceType": "Observation",
    "id": "sars-cov-2-rt-pcr-inconclusive",
    "meta": {
        "profile":  [
            "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr"
        ]
    },
    "identifier":  [
        {
            "type": {
                "coding":  [
                    {
                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
                        "code": "OBI"
                    }
                ]
            },
            "system": "https://www.charite.de/fhir/CodeSystem/lab-identifiers",
            "value": "94500-6_SARS-CoV-2-RNA-Presence-in-Respiratory-specimen",
            "assigner": {
                "reference": "Organization/Charité"
            }
        }
    ],
    "category":  [
        {
            "coding":  [
                {
                    "system": "http://loinc.org",
                    "code": "26436-6"
                },
                {
                    "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                    "code": "laboratory"
                }
            ]
        }
    ],
    "code": {
        "coding":  [
            {
                "code": "94500-6",
                "system": "http://loinc.org",
                "display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection"
            }
        ],
        "text": "SARS-CoV-2-RNA (PCR)"
    },
    "status": "final",
    "subject": {
        "reference": "Patient/gecco-patient"
    },
    "effectiveDateTime": "2020-10-16T08:49:21+02:00",
    "valueCodeableConcept": {
        "coding":  [
            {
                "code": "419984006",
                "system": "http://snomed.info/sct",
                "display": "Inconclusive (qualifier value)"
            }
        ],
        "text": "SARS-CoV-2-RNA nicht eindeutig"
    }
}