95609-4

SARS-CoV-2 (COVID-19) S gene [Presence] in Respiratory system specimen by Sequencing

Active

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.

Part Descriptions

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

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

LOINC Names Get Info

Fully-Specified Name: SARS coronavirus 2 S gene:PrThr:Pt:Respiratory System Specimen:Ord:Sequencing
Long Common Name: SARS-CoV-2 (COVID-19) S gene [Presence] in Respiratory system specimen by Sequencing
Short Name: SARS-CoV-2 S gene Resp Ql Seq
Display Name: SARS-CoV-2 (COVID-19) S gene Sequencing Ql (Respiratory system specimen)
Consumer Name Alpha Get Info: SARS-CoV-2 (COVID-19) S gene, Respiratory system specimen

Part Model Get Info

Component
SARS coronavirus 2 S gene
LP418046-1
- Analyte
  SARS coronavirus 2 S gene
  LP418046-1
  - Component Numerator
    SARS coronavirus 2 S gene
    LP418046-1
    - Component Numerator Core
      SARS coronavirus 2 S gene
      LP418046-1
    - Component Numerator Core Suffix
      NULL
  - Component Denominator
    NULL
    - Component Denominator Core
      NULL
    - Component Denominator Core Suffix
      NULL
- Challenge
  NULL
- Adjustment
  NULL
- Count
  NULL
Property
PrThr
LP217195-9
Time
Pt
LP6960-1
- Time Core
  Pt
  LP6960-1
- Time Modifier
  NULL
System
Respiratory System Specimen
LP436142-6
- System Core
  Respiratory System Specimen
  LP436142-6
- Super System
  NULL
Scale
Ord
LP7751-3
Method
Sequencing
LP150045-5

Example Answer List: LL5508-8

Source: Centers for Disease Control and Prevention

Answer	Code	Score	Answer ID
Detected			LA11882-0
Not detected			LA11883-8
InconclusiveCopyright http://snomed.info/sct ID:419984006 Inconclusive (qualifier value)			LA9663-1
InvalidCopyright 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 2.75 (MAJ)
Change Reason: Release 2.75: SYSTEM: There are 2 similar system's in LOINC: 1- Respiratory system 2- Respiratory specimen Due to an applied logic, the display in the System axis for 1 is Respiratory (adjective) without specification of sample, specimen, or other specific noun, while 2 is displayed fully as Respiratory specimen. Therefore for now we replaced 1 with Respiratory system specimen, which will affect 83 term. The result is replacing "Respiratory" with "Respiratory system specimen". This is the short approach. The bigger project is to potentially merge data that has either 1 or 2 together. This is a project to pass by the laboratory committee and will involve about 1500 concepts.;
Order vs. Observation: Both

Member of these Groups Get Info

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

Language Variants Get Info

Tag	Language	Translation
cs-CZ	Czech (Czechia)	SARS-CoV-2 (COVID-19) gen S:Přítomnost nebo práh:Časový bod:Vzorek z dýchacích cest:Ordinální:Sekvenace
de-DE	German (Germany)	SARS-Coronavirus 2 S-Gen:Nachweis oder Schwellenwert:Zeitpunkt:Probenmaterial vom Respirationstrakt:Ordinal:Sequenzierung
el-GR	Greek (Greece)	Γονίδιο S κορωνοϊού SARS 2:PrThr:Pt:Δείγμα αναπνευστικού συστήματος:Ord:Αλληλούχιση Synonyms: MICRO Ord PrThr Pt S Αλληλούχιση Αναπνευστικό Αναπνευστικό σύστημα Γονίδιο Γονίδιο S κορωνοϊού SARS 2 Δείγμα Δείγμα αναπνευστικού συστήματος Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2
es-ES	Spanish (Spain)	Gen S de SARS-CoV-2 (COVID-19):PrThr:Punto temporal:Muestra del sistema respiratorio:Ord:Secuenciación Synonyms: Muestra del tracto respiratorio Muestra respiratoria Tracto respiratorio
es-MX	Spanish (Mexico)	Gen del coronavirus 2 S del SARS:Presencia o umbral:Punto temporal:Espécimen respiratorio:Ordinal:Secuenciación
fr-FR	French (France)	Coronavirus SARS-CoV-2 gène S:Présence/Seuil:Ponctuel:Échantillon du système respiratoire:Qualitatif:Séquençage
fr-CA	French (Canada)	Coronavirus SARS-CoV-2 gène S:Présence-Seuil:Temps ponctuel:Échantillon du système respiratoire:Ordinal:Séquençage
it-IT	Italian (Italy)	SARS-CoV-2 (COVID-19), gene S:PrThr:Pt:Campione da Sistema Respiratorio:Ord:Sequenziamento Synonyms: Campione da Apparato Respiratorio Coronavirus della SARS Gene S di SARS-CoV-2 (COVID-19) Microbiologia Presenza o Soglia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NL	Dutch (Netherlands)	SARS-CoV-2 S-gen:aanwezigheid:moment:respiratoir monster:ordinaal:sequencing Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19 systema respiratorium; ademhalingsstelsel
pl-PL	Polish (Poland)	Gen S SARS-CoV-2 (COVID-19):granica wykrywalności:punkt w czasie:próbka z układu oddechowego:uporządkowany:sekwencjonowanie Synonyms: Koronawirus
zh-CN	Chinese (China)	SARS 冠状病毒 2 S 基因:存在情况或阈值:时间点:呼吸系统标本:序数型:序列测定 Synonyms: 2019 新型冠状病毒;2019 年新型冠状病毒;2019-nCoV;SARS-CoV-2;新型冠状病毒肺炎;新冠肺炎;Coronavirus disease 2019;COVID-19;冠状病毒疾病2019;严重急性呼吸综合征;severe acute respiratory syndrome;SARS;传染性非典型肺炎;infectious atypical pneumonia;非典 Ⅱ II S 型 SARS;SARS 病毒;SARS-CoV;严重急性呼吸综合征;严重急性呼吸综合征病毒;萨斯病毒;非典;非典型肺炎;非典型肺炎病毒;非典病毒供检查用的材料;待检物;待试验物;样品;样本;试料;试样依次型;分类顺序型;定性的;序数型（或称等级型）;性质上的;有序型;有序性分类应答;有序性分类结果;秩次型;等级型;筛查;顺序型受检物呼吸道标本（样品、样本）;呼吸系统标本（样品、样本）存在情况;存在;存在与否;是否存在;阈值;界值;界限;阀值;临界值;存在情况（存在、存在与否、是否存在）或阈值（界值、界限、阀值、临界值）序列分析;测序微生物学;微生物学试验;微生物学试验（培养、DNA、抗原及抗体）时刻;随机;随意;瞬间样品样本试样遗传基因;遗传因子;吉恩;生物基因

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Copyright © Regenstrief Institute, Inc. All Rights Reserved. To the extent included herein, the LOINC table and LOINC codes are copyright © Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee. See https://loinc.org/license for the full LOINC copyright and license.