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Term Description

Qualitative detection of nucleic acid from 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

LP417540-4   SARS coronavirus 2
The 2019 Novel Coronavirus (2019-nCoV) is a coronavirus first identified as the cause of a respiratory illness outbreak in Wuhan, China. Initially, the outbreak was linked to a large seafood and animal market and thought to only be spread by animal to person contact. Within a short time, a growing number of patients who had not been exposed to animal markets were diagnosed with the infection, indicating person-to-person transmission. As of January 2020, infections with 2019-nCoV had been reported internationally due to confirmed cases in travelers from Wuhan. Overall, clinical symptoms appear milder than SARS Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome (MERS) Coronavirus (MERS-CoV) infections as do the fatality rate and transmissibility. PMID: 31953166 Reported illnesses range from minor or no respiratory symptoms to severe acute respiratory illness and death.

The full genome of the 2019-nCoV 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. Source: LOINC

LOINC Names Get Info

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

Part Model Get Info

  • Component
    SARS coronavirus 2 RNA
    LP417541-2
    • Analyte
      SARS coronavirus 2 RNA
      LP417541-2
      • Component Numerator
        SARS coronavirus 2 RNA
        LP417541-2
        • Component Numerator Core
          SARS coronavirus 2
          LP417540-4
        • Component Numerator Core Suffix
          RNA
          LP32423-3
      • 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
  • 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: LL3250-9

Source: Association of Public Health Laboratories
AnswerCodeScoreAnswer ID
DetectedLA11882-0
Not detectedLA11883-8
InconclusiveCopyright http://snomed.info/sct ID:419984006 Inconclusive (qualifier value)LA9663-1
Specimen unsatisfactory for evaluationCopyright http://snomed.info/sct ID:125154007 Specimen unsatisfactory for evaluation (finding)LA13548-5

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 GroupGroup Name
LG50983-2SARS coronavirus 2 RNA|PrThr|Sys:ANYResp
LG51017-8SARSCoV2 detection
LG51019-4SARSCoV2 molecular detection

Language Variants Get Info

TagLanguageTranslation
cs-CZCzech (Czechia)SARS-CoV-2 (COVID-19) RNA:Přítomnost nebo práh:Časový bod:Vzorek z dýchacích cest:Ordinální:Sekvenace
de-DEGerman (Germany)SARS-Coronavirus 2 RNA:Nachweis oder Schwellenwert:Zeitpunkt:Probenmaterial vom Respirationstrakt:Ordinal:Sequenzierung
el-GRGreek (Greece)Κορωνοϊός SARS 2 RNA:PrThr:Pt:Δείγμα αναπνευστικού συστήματος:Ord:Αλληλούχιση
Synonyms: MICRO Ord PrThr Pt RNA Αλληλούχιση Αναπνευστικό Αναπνευστικό σύστημα Δείγμα Δείγμα αναπνευστικού συστήματος Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2
es-ESSpanish (Spain)Panel del SARS-CoV-2 (COVID-19) RNA:PrThr:Punto temporal:Muestra del sistema respiratorio:Ord:Secuenciación
Synonyms: Muestra del tracto respiratorio Muestra respiratoria Tracto respiratorio
es-MXSpanish (Mexico)ARN del coronavirus 2 del SARS:Presencia o umbral:Punto temporal:Espécimen respiratorio:Ordinal:Secuenciación
fr-FRFrench (France)Coronavirus SARS-CoV-2 ARN:Présence/Seuil:Ponctuel:Échantillon du système respiratoire:Qualitatif:Séquençage
fr-CAFrench (Canada)coronavirus 2 du SRAS ARN:Présence-Seuil:Temps ponctuel:Échantillon du système respiratoire:Ordinal:Séquençage
it-ITItalian (Italy)SARS coronavirus 2 RNA:PrThr:Pt:Campione da Sistema Respiratorio:Ord:Sequenziamento
Synonyms: Campione da Apparato Respiratorio Coronavirus della SARS Microbiologia Presenza o Soglia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NLDutch (Netherlands)SARS-CoV-2 RNA: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-PLPolish (Poland)SARS-CoV-2 RNA:granica wykrywalności:punkt w czasie:próbka z układu oddechowego:uporządkowany:sekwencjonowanie
Synonyms: Koronawirus
zh-CNChinese (China)SARS 冠状病毒 2 RNA: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 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 核糖核酸;Ribonucleic acid 试样

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CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=95424-8