Version 2.80

98062-3 Sequencing study identifier

Term Description

A unique identifier assigned by a lab for a sequencing study performed on a patient specimen. This identifier may be different from the unique identifier assigned to the original sample from the patient. The ID may also be provided to GISAID and reported to the Centers for Disease Control and Prevention (CDC) when submitting sequencing results for infectious pathogens, such as SARS coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic.

Fully-Specified Name

Component
Sequencing study identifier
Property
ID
Time
Pt
System
Specimen
Scale
Nom
Method

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.72 (MIN)
Order vs. Observation
Observation

Member of these Panels

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

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) Sequenzierungsidentifier:Identifikator:Zeitpunkt:Probenmaterial:Nominal:
el-GR Greek (Greece) Αναγνωριστικό μελέτης αλληλούχισης:Αναγνωριστικό:Pt:Δείγμα:Nom:
Synonyms: Αναγνωριστικό Αναγνωριστικό μελέτης αλληλούχισης Μελέτη
es-ES Spanish (Spain) Identificador del estudio de secuenciación:Código identificador:Punto temporal:Especimen:Nom:
es-MX Spanish (Mexico) Identificador del estudio de secuenciación:IDENTIFICACIÓN:Punto temporal:Muestra:Nominal:
fr-FR French (France) Séquençage identifiant:Identifiant:Ponctuel:Prélèvement:Résultat nominal:
it-IT Italian (Italy) Studio di sequenziamento, identificatore:ID:Pt:Campione:Nom:
Synonyms: Identificatore Identificatore di studio di sequenziamento Microbiologia Punto nel tempo (episodio)
nl-NL Dutch (Netherlands) identificator van sequencing-onderzoek:identificator:moment:monster:nominaal:
zh-CN Chinese (China) 序列测定检查标识符:标识符:时间点:标本:名义型:
Synonyms: 供检查用的材料;待检物;待试验物;样品;样本;试料;试样 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 受检物 序列测定（测序、序列分析）检查（检查项目）标识符（标识、ID） 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 标识;身份标识符;身份标识 标识;身份标识符;身份标识;ID 样品 样本 检查分析 研究;检查项目;调查;考察;研究项目;学习 考察 试样 调查

96766-1 GISAID sequence accession number

Term Description

GISAID Accession Numbers are unique and permanent identifiers for viral sequences. The GISAID numbers begin with letters EPI followed by a series of unique numbers. GISAID currently contains open-access genomic data for influenza viruses and SARS coronavirus 2 (SARS-CoV-2). Whole-genome sequences of SARS-CoV-2 were made available on GISAID beginning in January 2020 to enable global genomic epidemiology and real-time surveillance of new COVID-19 viral strains. [https://www.gisaid.org/]

Fully-Specified Name

Component
GISAID sequence accession number
Property
ID
Time
Pt
System
Isolate
Scale
Nom
Method

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.70 (ADD)
Order vs. Observation
Both

Member of these Panels

LOINC Long Common Name
101002-4 Monkeypox virus sequencing panel - Specimen by Sequencing
96894-1 SARS-CoV-2 (COVID-19) sequencing and identification panel - Specimen by Molecular genetics method

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) GISAID sequence accession-Nummer:Identifikator:Zeitpunkt:Isolat:Nominal:
el-GR Greek (Greece) Αριθμός υποβολής αλληλουχίας GISAID:Αναγνωριστικό:Pt:Απομονωμένο στέλεχος:Nom:
Synonyms: Αναγνωριστικό Αριθμός Αριθμός υποβολής αλληλουχίας GISAID
es-ES Spanish (Spain) Número de acceso a la secuencia GISAID:Código identificador:Punto temporal:Aislado:Nom:
es-MX Spanish (Mexico) Número de acceso a la secuencia GISAID:IDENTIFICACIÓN:Punto temporal:Aislar:Nominal:
fr-FR French (France) GISAID numéro d'incrément de séquence:Identifiant:Ponctuel:Isolat:Résultat nominal:
it-IT Italian (Italy) GISAID, numero di accessione alla sequenza:ID:Pt:Isolato:Nom:
Synonyms: Identificatore Microbiologia Numero di accessione alla sequenza GISAID Punto nel tempo (episodio)
zh-CN Chinese (China) GISAID 登录号:标识符:时间点:分离株:名义型:
Synonyms: GISAID 索取号;GISAID 记录号;GISAID 编录号;GISAID 序列号;病毒基因序列的永久性唯一标识符 个数;数目 分离物;分离菌;分离菌株;隔离种群 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 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 标识;身份标识符;身份标识 记录号;编录号;入藏号;索取号;序列号

94764-8 SARS-CoV-2 (COVID-19) whole genome [Nucleotide sequence] in Isolate or Specimen by Sequencing

Term Description

This term is used to report the sequence of the whole SARS coronavirus 2 (SARS-CoV-2) genome.

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

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 whole genome
Property
Seq
Time
Pt
System
Isolate/Specimen
Scale
Nom
Method
Sequencing

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.68
Last Updated
Version 2.69 (MAJ)
Change Reason
Release 2.69: SYSTEM: Updated System to "Isolate/Specimen" since the viral genome can be sequenced directly from a clinical specimen or from an isolate, and the sequence should be the same. ;
Order vs. Observation
Both

Member of these Panels

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

Member of these Groups Get Info

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

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 Gesamtgenom:Sequenz:Zeitpunkt:Isolat oder Probenmaterial:Nominal:Sequenzierung
el-GR Greek (Greece) Ολόκληρο γονιδίωμα του κορωνοϊού SARS 2:Seq:Pt:Απομονωθέν στέλεχος/Δείγμα:Nom:Αλληλούχιση
Synonyms: Seq Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Ολόκληρο γονιδίωμα του κορωνοϊού SARS 2
es-MX Spanish (Mexico) Genoma completo del coronavirus 2 del SARS:Secuencia de nucleótidos:Punto temporal:Aislado o espécimen:Nominal:Secuenciación
es-ES Spanish (Spain) Genoma completo del SARS-CoV-2 (COVID-19):Secuencia de nucleótidos:Punto temporal:Muestra aislada:Nom:Secuenciación
fr-FR French (France) Coronavirus SARS-CoV-2 génome entier:Séquence nucléotidique:Ponctuel:Isolat/échantillon:Résultat nominal:Séquençage
it-IT Italian (Italy) SARS coronavirus 2, intero genoma:Seq:Pt:Isolato/Campione:Nom:Sequenziamento
Synonyms: Coronavirus della SARS Intero genoma di SARS-CoV-2 (COVID-19) Isolato o Campione Microbiologia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19) Sequenza nucleotidica
nl-NL Dutch (Netherlands) geheel genoom van SARS-CoV-2:nucleotidevolgorde:moment:isolaat of monster:nominaal:sequencing
Synonyms: isolaat/specimen SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Cały genom SARS-CoV-2 (COVID-19):sekwencja nukleotydu:punkt w czasie:szczep/izolat lub próbka:cecha:sekwencjonowanie
Synonyms: Koronawirus
zh-CN Chinese (China) SARS 冠状病毒 2 全基因组:序列:时间点:分离株/标本: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 全（完整）基因组;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 供检查用的材料;待检物;待试验物;样品;样本;试料;试样 分离株/标本（样本、样品、试样） 分离物;分离菌;分离菌株;隔离种群 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 受检物 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 核苷酸序列 试样

96751-3 SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular genetics method

Term Description

This term is used to report the mutation(s) identified within the S (spike) gene of SARS coronavirus 2 (SARS-CoV-2) by molecular methods. 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 [LOINC: 96741-4]. To report the lineage for the variant, use SARS-CoV-2 (COVID-19) lineage [Type] in Specimen [LOINC: 96895-8]. To report the clade for the variant, use SARS-CoV-2 (COVID-19) clade [Type] in Specimen [LOINC: 96896-6].

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 S gene mutation detected
Property
Prid
Time
Pt
System
XXX
Scale
Nom
Method
Molgen

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.74 (MIN)
Change Reason
Release 2.74: ORDER_OBS: Updated to both an order and an observation for panel inclusion and representation as an order. ;
Order vs. Observation
Both

Example Answer List LL5775-3

Answer Code Score Answer ID
D614G LA31603-6
N501Y LA31604-4
K417N LA31605-1
E484K LA31606-9

Member of these Panels

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

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 S-Gen Mutation entdeckt:Nachweis oder Identität:Zeitpunkt:XXX:Nominal:Molekulargenetisch
el-GR Greek (Greece) Ανιχνεύθηκε μετάλλαξη γονιδίου S κορωνοϊού SARS 2:Prid:Pt:XXX:Nom:Μοριακή γενετική
Synonyms: Prid S Ανιχνεύθηκε μετάλλαξη γονιδίου S κορωνοϊού SARS 2 Γονίδιο Γονίδιο S κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Μετάλλαξη γονιδίου S κορωνοϊού SARS 2
es-MX Spanish (Mexico) Se detectó una mutación del gen S del coronavirus 2 del SARS:Orgullo:Punto temporal:No especificado:Nominal:Molgen
es-ES Spanish (Spain) Mutación detectada en el gen S del SARS-CoV-2 (COVID-19):Presencia o identidad:Punto temporal:XXX:Nom:Genética molecular
fr-FR French (France) Coronavirus SARS-CoV-2 mutation détectée du gène:Identification:Ponctuel:Milieux divers:Résultat nominal:Biologie moléculaire
it-IT Italian (Italy) SARS coronavirus 2, mutazione identificata del gene S:Prid:Pt:XXX:Nom:Molgen
Synonyms: Coronavirus della SARS Gene S di SARS-CoV-2 (COVID-19) Genetica molecolare Microbiologia Mutazione del gene S di SARS coronavirus 2;mutazione del gene S di SARS-CoV-2 (COVID-19) Mutazione identificata del gene S di SARS coronavirus 2;mutazione identificata del gene S di SARS-CoV-2 (COVID-19) Presenza o Identità Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NL Dutch (Netherlands) SARS-CoV-2 S-genmutatie aangetoond:identificator:moment:XXX:nominaal:moleculair genetisch onderzoek
Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Rozpoznana mutacja genu S SARS-CoV-2:wykrycie lub identyfikacja:punkt w czasie:XXX:cecha:genetyka molekularna
Synonyms: Koronawirus
zh-CN Chinese (China) 所检出的 SARS 冠状病毒 2 S 基因突变:存在与否或特征标识:时间点:XXX:名义型:分子遗传学类实验室方法
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 冠状病毒 2 S 基因突变;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 分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应 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 存在;存在与否;特征标识;身份;身份标识 微生物学;微生物学试验;微生物学试验（培养、DNA、抗原及抗体） 所检出的（所发现的、所检测出的） SARS 冠状病毒 2 S 基因突变;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 时刻;随机;随意;瞬间 遗传基因;遗传因子;吉恩;生物基因

96752-1 SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method

Term Description

This term is used to report whether a known mutation was detected within the S (spike) gene of SARS coronavirus 2 (SARS-CoV-2) by molecular methods. To report the mutation found, use [LOINC: 96751-3]. 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 [LOINC: 96741-4]. To report the lineage for the variant, use SARS-CoV-2 (COVID-19) lineage [Type] in Specimen [LOINC: 96895-8]. To report the clade for the variant, use SARS-CoV-2 (COVID-19) clade [Type] in Specimen [LOINC: 96896-6].

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 S gene mutation
Property
PrThr
Time
Pt
System
XXX
Scale
Ord
Method
Molgen

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.70 (ADD)
Order vs. Observation
Observation

Example Answer List LL744-4

Answer Code Score Answer ID
Detected LA11882-0
Not detected LA11883-8

Member of these Panels

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

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 S-Gen Mutation:Nachweis oder Schwellenwert:Zeitpunkt:XXX:Ordinal:Molekulargenetisch
el-GR Greek (Greece) Μετάλλαξη γονιδίου S κορωνοϊού SARS 2:PrThr:Pt:XXX:Ord:Μοριακή γενετική
Synonyms: PrThr S Γονίδιο Γονίδιο S κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Μετάλλαξη γονιδίου S κορωνοϊού SARS 2
es-MX Spanish (Mexico) Mutación del gen S del coronavirus 2 del SARS:PrThr:Punto temporal:No especificado:Ordinal:Molgen
es-ES Spanish (Spain) Mutación del gen S del SARS-CoV-2 (COVID-19):PrThr:Punto temporal:XXX:Ord:Genética molecular
fr-FR French (France) Coronavirus SARS-CoV-2 mutation du gène:Présence/Seuil:Ponctuel:Milieux divers:Qualitatif:Biologie moléculaire
it-IT Italian (Italy) SARS coronavirus 2, mutazione del gene S:PrThr:Pt:XXX:Ord:Molgen
Synonyms: Coronavirus della SARS Gene S di SARS-CoV-2 (COVID-19) Genetica molecolare Microbiologia Mutazione del gene S di SARS coronavirus 2;mutazione del gene S di SARS-CoV-2 (COVID-19) Presenza o Soglia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NL Dutch (Netherlands) SARS-CoV-2 S-genmutatie:aanwezigheid:moment:XXX:ordinaal:moleculair genetisch onderzoek
Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Mutacja genu S SARS-CoV-2:granica wykrywalności:punkt w czasie:XXX:półilościowy:genetyka molekularna
Synonyms: Koronawirus
zh-CN Chinese (China) SARS 冠状病毒 2 S 基因突变:存在情况或阈值:时间点:XXX:序数型:分子遗传学类实验室方法
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 冠状病毒 2 S 基因突变;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 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 分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应 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） 时刻;随机;随意;瞬间 遗传基因;遗传因子;吉恩;生物基因

96896-6 SARS-CoV-2 (COVID-19) clade [Type] in Specimen by Molecular genetics method

Term Description

SARS coronavirus 2 (SARS-CoV-2) clade assignment may be based on either the Nextstrain application [https://clades.nextstrain.org] or GISAID [https://www.gisaid.org/].

Part Descriptions

LP422736-1   SARS coronavirus 2 clade
Clade nomenclatures aim at providing a broad-brush categorization of globally circulating diversity of SARS-CoV-2. PMID: 32794443 One example of a Clade nomenclature is the based on year followed by a letter (Nextstrain.org). These are meant to be major groupings and not intended to completely specify genetic diversity. In general, new clades are proposed when certain criteria are met, for example reaching a frequency of 20% globally with at least two mutations away from its parent clade.[https://virological.org/t/year-letter-genetic-clade-naming-for-sars-cov-2-on-nextstrain-org/498] Source: Regenstrief LOINC

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 clade
Property
Type
Time
Pt
System
XXX
Scale
Nom
Method
Molgen

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.72 (MIN)
Order vs. Observation
Observation

Example Answer List LL5806-6

Answer Code Score Answer ID
SARS-CoV-2 clade 19A LA31687-9
SARS-CoV-2 clade 19B LA31688-7
SARS-CoV-2 clade 20A LA31689-5
SARS-CoV-2 clade 20B LA31690-3
SARS-CoV-2 clade 20C LA31691-1
SARS-CoV-2 clade 20D LA31692-9
SARS-CoV-2 clade 20E LA31693-7
SARS-CoV-2 clade 20F LA31694-5
SARS-CoV-2 clade 20G LA31695-2
SARS-CoV-2 clade 20H LA31696-0
SARS-CoV-2 clade 20I LA31697-8
SARS-CoV-2 clade 20J LA31698-6

Member of these Panels

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

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 Klade:Typ:Zeitpunkt:XXX:Nominal:Molekulargenetisch
el-GR Greek (Greece) Κλάδος κορωνοϊού SARS 2:Type:Pt:XXX:Nom:Μοριακή γενετική
Synonyms: Type Κλάδος κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2
es-MX Spanish (Mexico) SARS coronavirus 2 clado:Escribe:Punto temporal:No especificado:Nominal:Molgen
es-ES Spanish (Spain) Clado de SARS-CoV-2 (COVID-19):Tipo:Punto temporal:XXX:Nom:Genética molecular
fr-FR French (France) Coronavirus SARS-CoV-2 clade:Type:Ponctuel:Milieux divers:Résultat nominal:Biologie moléculaire
it-IT Italian (Italy) SARS coronavirus 2 clade:Tipo:Pt:XXX:Nom:Molgen
Synonyms: Coronavirus della SARS Genetica molecolare Microbiologia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19) SARS-CoV-2 (COVID-19) clade
nl-NL Dutch (Netherlands) SARS-CoV-2 clade:type:moment:XXX:nominaal:moleculair genetisch onderzoek
Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Klad SARS-CoV-2:typ:punkt w czasie:XXX:cecha:genetyka molekularna
Synonyms: Koronawirus
zh-CN Chinese (China) SARS 冠状病毒 2 进化枝:类型:时间点:XXX:名义型:分子遗传学类实验室方法
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 进化枝（分支、支、支系、分枝、分化体、种系分枝、演化支）;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 分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应 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 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

96895-8 SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method

Term Description

SARS coronavirus 2 (SARS-CoV-2) lineage determine by molecular genetic methods, such as sequencing or PCR. Results may be determined using the Pangolin lineage assignment application [https://cov-lineages.org/pangolin.html] or another lineage classification.

Part Descriptions

LP422739-5   SARS coronavirus 2 lineage
Lineage nomenclatures are intended to provide a detailed level differentiation of viral mutations of SARS-CoV-2 over time. However, proposed lineage nomenclatures are not intended to portray every evolutionary change, but rather those associated with important epidemiological and biological events. PMID: 32669681 That being said they are not as broad-brushed as clades, but are expected to correspond to outbreaks. PMID: 32794443 Source: Regenstrief LOINC

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 lineage
Property
Prid
Time
Pt
System
XXX
Scale
Nom
Method
Molgen

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.72 (MIN)
Change Reason
Release 2.72: DefinitionDescription: Updated description to clarify that this term is not specific to Pangolin lineage only.;
Order vs. Observation
Observation

Example Answer List LL5807-4

Answer Code Score Answer ID
SARS-CoV-2 A.1.1 lineage LA31701-8
SARS-CoV-2 B.1.1.238 lineage LA31620-0
SARS-CoV-2 B.1.2 lineage LA31703-4
SARS-CoV-2 B.1.1 lineage LA31704-2
SARS-CoV-2 B.1.1.7 lineage LA31705-9
SARS-CoV-2 B.1.29 lineage LA31706-7
SARS-CoV-2 B.2.4 lineage LA31702-6
SARS-CoV-2 B.1.351 lineage LA32553-2
SARS-CoV-2 P.1 lineage LA32555-7
SARS-CoV-2 B.1.617.2 lineage LA32556-5

Member of these Panels

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

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 Abstammungslinie:Nachweis oder Identität:Zeitpunkt:XXX:Nominal:Molekulargenetisch
el-GR Greek (Greece) Γενεαλογική σειρά κορωνοϊού SARS 2:Prid:Pt:XXX:Nom:Μοριακή γενετική
Synonyms: Prid Γενεαλογική σειρά κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2
es-ES Spanish (Spain) Linaje de SARS-CoV-2 (COVID-19):Presencia o identidad:Punto temporal:XXX:Nom:Genética molecular
es-MX Spanish (Mexico) Linaje del coronavirus 2 del SARS:Orgullo:Punto temporal:No especificado:Nominal:Molgen
fr-FR French (France) Coronavirus SARS-CoV-2 lignée:Identification:Ponctuel:Milieux divers:Résultat nominal:Biologie moléculaire
it-IT Italian (Italy) SARS coronavirus 2, lignaggio:Prid:Pt:XXX:Nom:Molgen
Synonyms: Coronavirus della SARS Genetica molecolare Lignaggio di SARS-CoV-2 (COVID-19) Microbiologia Presenza o Identità Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NL Dutch (Netherlands) SARS-CoV-2 lineage:identificator:moment:XXX:nominaal:moleculair genetisch onderzoek
Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Linia rodowodowa SARS-CoV-2:wykrycie lub identyfikacja:punkt w czasie:XXX:cecha:genetyka molekularna
Synonyms: Koronawirus
zh-CN Chinese (China) SARS 冠状病毒 2 谱系:存在与否或特征标识:时间点:XXX:名义型:分子遗传学类实验室方法
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 谱系（世系、血统、宗系、家系、种系）;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 分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应 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 存在;存在与否;特征标识;身份;身份标识 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

96741-4 SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing

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 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

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 variant
Property
Type
Time
Pt
System
XXX
Scale
Nom
Method
Sequencing

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

Example Answer List LL5768-8

Answer Code Score Answer ID
SARS-CoV-2 Alpha variant (WHO) LA31569-9
SARS-CoV-2 Beta variant (WHO) LA31570-7
SARS-CoV-2 Gamma variant (WHO) LA31621-8
SARS-CoV-2 Delta variant (WHO) LA32552-4
SARS-CoV-2 Omicron variant (WHO) LA33381-7

Member of these Panels

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

Member of these Groups Get Info

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

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2-Variante:Typ:Zeitpunkt:XXX:Nominal:Sequenzierung
de-AT German (Austria) Synonyms: SARS-CoV-2 Mutationsscreening ql. /SM
el-GR Greek (Greece) Παραλλαγή κορωνοϊού SARS 2:Type:Pt:XXX:Nom:Αλληλούχιση
Synonyms: Type Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Παραλλαγή κορωνοϊού SARS 2
es-MX Spanish (Mexico) Variante del coronavirus 2 del SARS:Escribe:Punto temporal:No especificado:Nominal:Secuenciación
es-ES Spanish (Spain) Variante del SARS-CoV-2 (COVID-19):Tipo:Punto temporal:XXX:Nom:Secuenciación
fr-FR French (France) Coronavirus SARS-CoV-2 variant:Type:Ponctuel:Milieux divers:Résultat nominal:Séquençage
fr-CA French (Canada) Variants du SRAS Coronavirus 2:Type:Temps ponctuel:XXX:Nominal:Séquençage
it-IT Italian (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-NL Dutch (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-PL Polish (Poland) Wariant SARS-CoV-2:typ:punkt w czasie:XXX:cecha:sekwencjonowanie
Synonyms: Koronawirus
zh-CN Chinese (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

96755-4 SARS-CoV-2 (COVID-19) variant interpretation in Specimen Narrative

Term Description

The interpretation of the genetic variant(s) identified and association with variants of concern (VOC).

Reference Information

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

Fully-Specified Name

Component
SARS coronavirus 2 variant interpretation
Property
Imp
Time
Pt
System
XXX
Scale
Nar
Method

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.70 (ADD)
Order vs. Observation
Observation

Member of these Panels

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

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 Varianteninterpretation:Interpretation:Zeitpunkt:XXX:Freitext:
el-GR Greek (Greece) Ερμηνεία παραλλαγής κορωνοϊού SARS 2:Imp:Pt:XXX:Nar:
Synonyms: Imp Ερμηνεία Ερμηνεία παραλλαγής κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Παραλλαγή κορωνοϊού SARS 2
es-ES Spanish (Spain) Interpretación de la variante del SARS-CoV-2 (COVID-19):Impresión/interpretación del estudio:Punto temporal:XXX:Narrativo:
es-MX Spanish (Mexico) Interpretación de la variante del coronavirus 2 del SARS:Diablillo:Punto temporal:No especificado:Narrativo:
fr-FR French (France) Coronavirus SARS-CoV-2 variant - Interprétation:Interprétation:Ponctuel:Milieux divers:Résultat textuel:
it-IT Italian (Italy) SARS coronavirus 2, interpretazione variante:Imp:Pt:XXX:Nar:
Synonyms: Coronavirus della SARS Impressione/interpretazione di studio Interpretazione variante di SARS coronavirus 2;Interpretazione variante di SARS-CoV-2 (COVID-19) Microbiologia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19) Variante di SARS coronavirus 2;variante di SARS-CoV-2 (COVID-19)
nl-NL Dutch (Netherlands) SARS-CoV-2-variant interpretatie:interpretatie:moment:XXX:tekstueel:
Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
zh-CN Chinese (China) SARS 冠状病毒 2 变异解释:印象:时间点:XXX:叙述型:
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 冠状病毒 2 变异（变异株、变异毒株）解释（说明）;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 判读;解释说明;说明;释义;阐明 印象是一种诊断陈述，始终是对其他某种观察指标的解释或抽象（一系列检验项目结果、一幅图像或者整个某位病人），而且几乎总是由某位专业人员产生。;检查印象;检查印象/解释;检查的印象/解释;检查解释;解释;阐释 叙述;叙述性文字;报告;报告型;文字叙述;文本叙述型;文本描述;文本描述型 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