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Term Description

For reporting the SARS-CoV-2 variant strain identified, various codes are available in LOINC depending on the nomenclature used. For the most general code (nomenclature unspecified), use SARS-CoV-2 (COVID-19) variant [Type] in specimen by sequencing (this term) or by nucleic acid amplification (NAA) with probe-based detection LOINC 100156-9. To report the lineage for the variant, use SARS-CoV-2 (COVID-19) lineage [Type] in Specimen LOINC 96895-8 (method unspecified). To report the clade for the variant, use SARS-CoV-2 (COVID-19) clade [Type] in Specimen LOINC 96896-6 (method unspecified).

Part Description

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

LOINC Names Get Info

Fully-Specified Name
SARS coronavirus 2 variant:Type:Pt:XXX:Nom:Sequencing
Long Common Name
SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing
Short Name
SARS-CoV-2 variant Spec Seq
Display Name
SARS-CoV-2 (COVID-19) variant Sequencing Nom (Specimen)
Consumer Name Alpha Get Info
SARS-CoV-2 (COVID-19) variant, Specimen

Part Model Get Info

  • Component
    SARS coronavirus 2 variant
    LP422125-7
    • Analyte
      SARS coronavirus 2 variant
      LP422125-7
      • Component Numerator
        SARS coronavirus 2 variant
        LP422125-7
        • Component Numerator Core
          SARS coronavirus 2 variant
          LP422125-7
        • Component Numerator Core Suffix
          NULL
           
      • Component Denominator
        NULL
         
        • Component Denominator Core
          NULL
           
        • Component Denominator Core Suffix
          NULL
           
    • Challenge
      NULL
       
    • Adjustment
      NULL
       
    • Count
      NULL
       
  • Property
    Type
    LP6886-8
  • Time
    Pt
    LP6960-1
  • System
    XXX
    LP7735-6
    • System Core
      XXX
      LP7735-6
    • Super System
      NULL
       
  • Scale
    Nom
    LP7750-5
  • Method
    Sequencing
    LP150045-5

Example Answer List: LL5768-8

Source: World Health Organization (WHO)
AnswerCodeScoreAnswer ID
SARS-CoV-2 Alpha variant (WHO)

Also known as B.1.1.7, 20I/501Y.V1, VOC - 202012/01, and UK variant

LA31569-9
SARS-CoV-2 Beta variant (WHO)

Also known as B.1.351, 501Y.V2, and South Africa variant

LA31570-7
SARS-CoV-2 Gamma variant (WHO)

Also known as P.1 lineage, 501Y.V3, and 20J/501Y.V3

LA31621-8
SARS-CoV-2 Delta variant (WHO)

Also known as G/478K.V1, Nextstrain clade 21A, and B.1.617.2 lineage

LA32552-4
SARS-CoV-2 Omicron variant (WHO)

Also known as B.1.1.529

LA33381-7

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.77 (MIN)
Change Reason
Release 2.77: DefinitionDescription: replaced [LOINC: TBD] with 100156-9 ;
Order vs. Observation
Both

Member of these Panels

LOINCLong Common Name
96894-1SARS-CoV-2 (COVID-19) sequencing and identification panel - Specimen by Molecular genetics method

Member of these Groups Get Info

LOINC GroupGroup Name
LG51017-8SARSCoV2 detection
LG51019-4SARSCoV2 molecular detection

Language Variants Get Info

TagLanguageTranslation
cs-CZCzech (Czechia)SARS-CoV-2 (COVID-19) varianta:Typ:Časový bod:XXX:Nominální:Sekvenace
de-ATGerman (Austria)Synonyms: SARS-CoV-2 Mutationsscreening ql. /SM
de-DEGerman (Germany)SARS-Coronavirus 2-Variante:Typ:Zeitpunkt:XXX:Nominal:Sequenzierung
el-GRGreek (Greece)Παραλλαγή κορωνοϊού SARS 2:Type:Pt:XXX:Nom:Αλληλούχιση
Synonyms: MICRO Nom Pt Type XXX Αλληλούχιση Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Παραλλαγή κορωνοϊού SARS 2
es-ESSpanish (Spain)Variante del SARS-CoV-2 (COVID-19):Tipo:Punto temporal:XXX:Nom:Secuenciación
es-MXSpanish (Mexico)Variante del coronavirus 2 del SARS:Escribe:Punto temporal:No especificado:Nominal:Secuenciación
fr-FRFrench (France)Coronavirus SARS-CoV-2 variant:Type:Ponctuel:Milieux divers:Résultat nominal:Séquençage
fr-CAFrench (Canada)Variants du SRAS Coronavirus 2:Type:Temps ponctuel:XXX:Nominal:Séquençage
it-ITItalian (Italy)SARS coronavirus 2, variante:Tipo:Pt:XXX:Nom:Sequenziamento
Synonyms: Coronavirus della SARS Microbiologia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19) Variante di SARS coronavirus 2 variante di SARS-CoV-2 (COVID-19)
nl-NLDutch (Netherlands)SARS-CoV-2-variant:type:moment:XXX:nominaal:sequencing
Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PLPolish (Poland)Wariant SARS-CoV-2:typ:punkt w czasie:XXX:skala nominalna:sekwencjonowanie
Synonyms: Koronawirus wynik kategorialny
zh-CNChinese (China)SARS 冠状病毒 2 变异:类型:时间点:XXX:名义型: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 冠状病毒 2 变异（变异株、变异毒株）;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 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 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 分类型应答;分类型结果;名义性;名称型;名词型;名词性;标称性;没有自然次序的名义型或分类型应答 型 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

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

CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=96741-4