LOINC
Version 2.73

95609-4SARS-CoV-2 (COVID-19) S gene [Presence] in Respiratory specimen by SequencingActive

Term Description

Qualitative detection of nucleic acids within the spike (S) gene of SARS coronavirus 2 (SARS-CoV-2) in respiratory specimens by sequencing methods, such as next generation sequencing (NGS), also known as high-throughput sequencing (HTS). Testing is performed for the diagnosis of COVID-19.
Source: Regenstrief LOINC

Part Descriptions

LP418046-1   SARS coronavirus 2 S gene
The Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), first known as 2019 Novel Coronavirus (2019-nCoV), was first identified as the cause of a respiratory illness outbreak, later defined as Coronavirus Disease 2019 (COVID-19), in Wuhan, China. The full genome of the SARS-CoV-2 that causes COVID-19 was first posted by Chinese health authorities in GenBank, the NIH genetic sequence database, and in the Global Initiative on Sharing All Influenza Data (GISAI) portal. This facilitated detection of the virus globally with subsequent sequences being nearly identical, suggesting a single, recent emergence from a virus related to bat coronaviruses and the SARS coronavirus. Real time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR) tests targeting regions within genes, including RdRp, S, N, M, and E genes, specific to SARS-CoV-2 have been developed by the Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO) and others for the diagnosis of COVID-19. Some assays only detect SARS-CoV-2 and other assays detect other strains (e.g. SARS-CoV) that are genetically similar.[CDC:coronavirus/2019-ncov][https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance] Source: Regenstrief LOINC

LP150045-5   Sequencing
Sequencing is a method used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes. Historically, most sequencing has been performed using the chain termination method developed by Frederick Sanger in 1977.[PMID:271968] Sequencing technologies have improved dramatically, making them cheaper, faster, and more accurate. Next-generation sequencing (NGS), also known as high-throughput sequencing, deep sequencing, and second-generation sequencing, is a type of technology that uses parallel sequencing of multiple small fragments of DNA to determine sequence. This "high-throughput" technology has increased the speed and amount of DNA sequenced at a significantly reduced cost.[PMID:18576944] Several NGS platforms (ie, sequencing instruments and associated reagents) have been developed. Third-generation sequencing is another methodology currently under development that uses parallel sequencing similar to NGS. In contrast to NGS, third-generation sequencing uses single DNA molecules rather than amplified DNA as a template.[PMID:20858600] Source: Regenstrief LOINC

Fully-Specified Name

Component
SARS coronavirus 2 S gene
Property
PrThr
Time
Pt
System
Respiratory
Scale
Ord
Method
Sequencing

Additional Names

Short Name
SARS-CoV-2 S gene Resp Ql Seq
Display Name
SARS-CoV-2 (COVID-19) S gene Sequencing Ql (Resp)
Consumer Name Alpha
SARS-CoV-2 (COVID-19) S gene, Respiratory

Example Answer List LL5508-8

Source: Centers for Disease Control and Prevention

Answer Code Score Answer ID
Detected LA11882-0
Not detected LA11883-8
Inconclusive Copyright http://snomed.info/sct ID:419984006 Inconclusive (qualifier value) LA9663-1
Invalid Copyright http://snomed.info/sct ID:455371000124106 Invalid result (qualifier value) LA15841-2

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.69
Last Updated
Version 2.69
Order vs. Observation
Both

Reference Information

Type Source Reference
Webcontent Lab Tests Online®Copyright Copyright © 2021 Lab Tests Online. All rights reserved. Coronavirus (COVID-19) Testing

Member of these Groups

LG51033-5 SARS coronavirus 2 S gene|PrThr|Sys:ANYResp
LG51017-8 SARSCoV2 detection
LG51019-4 SARSCoV2 molecular detection

Language Variants Get Info

zh-CNChinese (China)
SARS 冠状病毒 2 S 基因:存在情况或阈值:时间点:呼吸道:序数型:序列测定
nl-NLDutch (Netherlands)
SARS-CoV-2 S-gen:aanwezigheid:moment:luchtwegen:ordinaal:sequencing
fr-CAFrench (Canada)
gène S du coronavirus 2 du SRAS:Présence-Seuil:Temps ponctuel:Respiratoire:Ordinal:Séquençage
fr-FRFrench (France)
Coronavirus SARS-CoV-2 gène S:Présence/Seuil:Ponctuel:Respiratoire:Qualitatif:Séquençage
de-DEGerman (Germany)
SARS-Coronavirus 2 S-Gen:Nachweis oder Schwellenwert:Zeitpunkt:Respirationstrakt:Ordinal:Sequenzierung
it-ITItalian (Italy)
SARS-CoV-2 (COVID-19), gene S:PrThr:Pt:Respiratorio:Ord:Sequenziamento
pl-PLPolish (Poland)
gen S SARS-CoV-2 (COVID-19):obecność lub wartość progowa:Punkt w czasie:próbka z dróg oddechowych:Porządkowy:Sekwencjonowanie
es-MXSpanish (Mexico)
Gen del coronavirus 2 S del SARS:Presencia o umbral:Punto temporal:Espécimen respiratorio:Ordinal:Secuenciación
es-ESSpanish (Spain)
Gen S de SARS-CoV-2 (COVID-19):PrThr:Punto temporal:Respiratorio:Ord:Secuenciación

LOINC FHIR® API Example - CodeSystem Request Get Info

https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=95609-4