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Term Description

Qualitative detection of nucleic acids within the envelope (E) gene of SARS coronavirus 2 (SARS-CoV-2) in saliva specimens by nucleic acid amplification with probe-based detection. Testing is performed for the diagnosis of COVID-19.

Part Descriptions

LP417600-6   SARS-related coronavirus E 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

LP7565-7   Saliva
Saliva is produced primarily by the parotid, submaxillary, and sublingual glands. It is secreted at the rate of 0-3 milliliters per minute which is affected by various factors including anxiety, hydration and hunger. Oral fluid is broadly used to test for drugs of abuse in employment and forensic settings, and is especially useful since it is difficult to adulterate, is quick and is non-invasive. Oral fluid is used to test a variety of analytes, including to test alcohol, HIV and other antibodies, therapeutic drugs and steroids, but its primary use is to test for drugs of abuse including amphetamines, cocaine and metabolites, opioids, methadone, cannabis and heroin. PMID: 17268583 Source: Regenstrief LOINC

Reference Information

TypeSourceReference
Mapping GuidanceLOINCTake caution when mapping LOINC codes to molecular tests for SARS coronaviruses that target nucleic acids within the E gene. Such assays detect either SARS-related coronavirus or SARS-CoV-2, depending on the targeted region within the E gene. Assays that are non-specific to only SARS-CoV-2 may say they are "positive" for SARS-CoV-2, but only because it is the primary circulating virus during the pandemic. These assays actually detect any SARS-related coronaviruses since they target a region in the E gene that contains sequence homology to other known coronaviruses. Other assays target a region in the E gene that is specific for SARS-CoV-2. The LIVD file contains current LOINC code mappings to many IVD tests https://www.cdc.gov/csels/dls/sars-cov-2-livd-codes.html. You may also contact the manufacturer directly to verify LOINC code mappings.

LOINC Names Get Info

Fully-Specified Name
SARS-related coronavirus E gene:PrThr:Pt:Saliva:Ord:Probe.amp.tar
Long Common Name
SARS-related coronavirus E gene [Presence] in Saliva (oral fluid) by NAA with probe detection
Short Name
SARS-rel CoV E gene Sal Ql NAA+probe
Display Name
SARS-related coronavirus E gene NAA+probe Ql (Sal)
Consumer Name Alpha Get Info
SARS-related coronavirus E gene, Saliva

Part Model Get Info

  • Component
    SARS-related coronavirus E gene
    LP417600-6
    • Analyte
      SARS-related coronavirus E gene
      LP417600-6
      • Component Numerator
        SARS-related coronavirus E gene
        LP417600-6
        • Component Numerator Core
          SARS-related coronavirus E gene
          LP417600-6
        • 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
  • System
    Saliva
    LP7565-7
    • System Core
      Saliva
      LP7565-7
    • Super System
      NULL
       
  • Scale
    Ord
    LP7751-3
  • Method
    Probe.amp.tar
    LP6464-4

Example Answer List: LL5508-8

Source: Centers for Disease Control and Prevention
AnswerCodeScoreAnswer ID
DetectedLA11882-0
Not detectedLA11883-8
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 2.69 (ADD)
Order vs. Observation
Observation

Member of these Panels

LOINCLong Common Name
98080-5SARS-CoV-2 (COVID-19) and SARS-related CoV RNA panel - Saliva (oral fluid) by NAA with probe detection
95826-4SARS-CoV-2 (COVID-19) RNA panel - Saliva (oral fluid) by NAA with probe detection

Member of these Groups Get Info

LOINC GroupGroup Name
LG50982-4SARS-related coronavirus

Language Variants Get Info

TagLanguageTranslation
cs-CZCzech (Czechia)Koronavirus související se SARS gen E:Přítomnost nebo práh:Časový bod:Sliny:Ordinální:Amplifikace nukleových kyselin s detekcí sondou
de-DEGerman (Germany)SARS-bezogenes Coronavirus E-Gen:Nachweis oder Schwellenwert:Zeitpunkt:Speichel:Ordinal:Zielfragmentamplifikation mit Sondendetektion
el-GRGreek (Greece)Γονίδιο Ε κορονοϊού που σχετίζεται με το SARS:PrThr:Pt:Σίελος:Ord:Ανιχνευτής.ενίσχυση.στόχου
Synonyms: E MICRO Ord PrThr Pt Ανιχνευτής Ανιχνευτής.ενίσχυση Ανιχνευτής.ενίσχυση.στόχου Γονίδιο Γονίδιο Ε κορονοϊού που σχετίζεται με το SARS Κορωνοϊός Κορωνοϊός που σχετίζεται με το SARS Σίελος
es-ESSpanish (Spain)Gen del coronavirus E relacionado con el SARS:PrThr:Punto temporal:Saliva:Ord:Sonda con amplificación dirigida
es-MXSpanish (Mexico)Gen del coronavirus E relacionado con el SARS:Presencia o umbral:Punto temporal:Saliva:Ordinal:Amplificación de ácidos nucleicos con detección de sonda
fr-CAFrench (Canada)Gène E du coronavirus lié du SRAS:Présence-Seuil:Temps ponctuel:Salivaire:Ordinal:Sonde avec amplification de la cible
fr-FRFrench (France)Coronavirus SARS apparentés gène E:Présence/Seuil:Ponctuel:Salive:Qualitatif:PCR amplification de cible
it-ITItalian (Italy)Coronavirus correlato a SARS, gene E:PrThr:Pt:Saliva:Ord:Sonda.amp.tar
Synonyms: Gene E di coronavirus correlato a SARS Microbiologia Presenza o Soglia Punto nel tempo (episodio) Sonda con amplificazione Sonda con amplificazione del target Sonda di DNA
nl-NLDutch (Netherlands)SARS-gerelateerd coronavirus E-gen:aanwezigheid:moment:speeksel:ordinaal:probe-detectie
Synonyms: probe.amp.tar
pl-PLPolish (Poland)Koronawirus związany z SARS gen E:granica wykrywalności:punkt w czasie:ślina:uporządkowany:sonda.amplifikacja.cel
Synonyms: amplifikacja kwasu nukleinowego z detekcją za pomocą sondy amplifikacja z detekcją za pomocą sondy Koronawirus SARSr-CoV SARSr-CoV gen E
zh-CNChinese (China)SARS 冠状病毒 2 E 基因:存在情况或阈值:时间点:唾液:序数型:探针法.基因扩增.靶向
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 E 型 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 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 借助扩增的探针方法;借助扩增的探针法;探针法.扩增 借助靶向扩增的探针方法;借助靶向扩增的探针法;探针法.扩增.靶向 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） 微生物学;微生物学试验;微生物学试验（培养、DNA、抗原及抗体） 扩增型 扩增性 时刻;随机;随意;瞬间 津;津液;涎 经过扩增的 脱氧核糖核酸探针 遗传基因;遗传因子;吉恩;生物基因

LOINC Terminology Service (API) using HL7® FHIR® Get Info

CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=95823-1