96894-1
SARS-CoV-2 (COVID-19) sequencing and identification panel - Specimen by Molecular genetics method
Active
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | Sequencing identifikátor studie: |
| de-DE | German (Germany) | Identifikator der Sequenzierungs-Untersuchung: Synonyms: Sequenzierungsidentifikator; |
| el-GR | Greek (Greece) | Αναγνωριστικό μελέτης αλληλούχισης: Synonyms: MICRO Nom Pt Αναγνωριστικό Αναγνωριστικό μελέτης αλληλούχισης Δείγμα Μελέτη |
| es-ES | Spanish (Spain) | Identificador del estudio de secuenciación: |
| es-MX | Spanish (Mexico) | Identificador del estudio de secuenciación: |
| fr-FR | French (France) | Séquençage identifiant: |
| it-IT | Italian (Italy) | Studio di sequenziamento, identificatore: Synonyms: Identificatore Identificatore di studio di sequenziamento Microbiologia Punto nel tempo (episodio) |
| nl-NL | Dutch (Netherlands) | identificator van sequencing-onderzoek: |
| pl-PL | Polish (Poland) | Identyfikator badania wykonanego metodą sekwencjonowania: Synonyms: wynik kategorialny |
| zh-CN | Chinese (China) | 序列测定检查标识符: Synonyms: 供检查用的材料; |
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | GISAID přístupové číslo sekvence: |
| de-DE | German (Germany) | GISAID sequence accession-Nummer: |
| el-GR | Greek (Greece) | Αριθμός υποβολής αλληλουχίας GISAID: Synonyms: MICRO Nom Pt Αναγνωριστικό Απομονωμένο στέλεχος Αριθμός Αριθμός πρόσβασης Αριθμός υποβολής αλληλουχίας GISAID |
| es-ES | Spanish (Spain) | Número de acceso a la secuencia GISAID: |
| es-MX | Spanish (Mexico) | Número de acceso a la secuencia GISAID: |
| fr-FR | French (France) | GISAID numéro d'incrément de séquence: |
| it-IT | Italian (Italy) | GISAID, numero di accessione alla sequenza: Synonyms: Identificatore Microbiologia Numero di accessione alla sequenza GISAID Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Numer dostępu do sekwencji GISAID: Synonyms: wynik kategorialny |
| zh-CN | Chinese (China) | GISAID 登录号: Synonyms: GISAID 索取号; |
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
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) celý genom: |
| de-DE | German (Germany) | SARS-Coronavirus 2 Gesamtgenom: |
| el-GR | Greek (Greece) | Ολόκληρο γονιδίωμα του κορωνοϊού SARS 2: Synonyms: MICRO Nom Pt Seq Αλληλούχιση Απομονωθέν στέλεχος/Δείγμα Απομονωμένο στέλεχος Δείγμα Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Ολόκληρο γονιδίωμα του κορωνοϊού SARS 2 |
| es-ES | Spanish (Spain) | Genoma completo del SARS-CoV-2 (COVID-19): |
| es-MX | Spanish (Mexico) | Genoma completo del coronavirus 2 del SARS: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 génome entier: |
| it-IT | Italian (Italy) | SARS coronavirus 2, intero genoma: 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: Synonyms: isolaat/specimen SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Cały genom SARS-CoV-2 (COVID-19): Synonyms: Koronawirus wynik kategorialny |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 全基因组: Synonyms: 2019 新型冠状病毒; |
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.
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) gen S mutace detekována: |
| de-DE | German (Germany) | SARS-Coronavirus 2 S-Gen Mutation entdeckt: |
| el-GR | Greek (Greece) | Ανιχνεύθηκε μετάλλαξη γονιδίου S κορωνοϊού SARS 2: Synonyms: MICRO Nom Prid Pt S XXX 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 Μοριακή γενετική |
| es-ES | Spanish (Spain) | Mutación detectada en el gen S del SARS-CoV-2 (COVID-19): |
| es-MX | Spanish (Mexico) | Se detectó una mutación del gen S del coronavirus 2 del SARS: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 mutation détectée du gène: |
| it-IT | Italian (Italy) | SARS coronavirus 2, mutazione identificata del gene S: 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: Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Rozpoznana mutacja genu S SARS-CoV-2: Synonyms: diagnostyka molekularna Koronawirus wynik kategorialny |
| zh-CN | Chinese (China) | 所检出的 SARS 冠状病毒 2 S 基因突变: Synonyms: 2019 新型冠状病毒; |
96752-1 SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molgen
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.
Fully-Specified Name
- Component
- SARS coronavirus 2 S gene mutation
- Property
- PrThr
- Time
- Pt
- System
- {Specimen}
- Scale
- Ord
- Method
- {Molgen}
Basic Attributes
- Class
- MICRO
- Type
- Laboratory
- First Released
- Version 2.70
- Last Updated
- Version 2.83 (MAJ)
- 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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) gen S mutace: |
| de-DE | German (Germany) | SARS-Coronavirus 2 S-Gen Mutation: |
| el-GR | Greek (Greece) | Μετάλλαξη γονιδίου S κορωνοϊού SARS 2: Synonyms: MICRO Ord PrThr Pt S XXX Γονίδιο Γονίδιο S κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Μετάλλαξη γονιδίου S κορωνοϊού SARS 2 Μοριακή γενετική |
| es-MX | Spanish (Mexico) | Mutación del gen S del coronavirus 2 del SARS: |
| es-ES | Spanish (Spain) | Mutación del gen S del SARS-CoV-2 (COVID-19): |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 mutation du gène: |
| it-IT | Italian (Italy) | SARS coronavirus 2, mutazione del gene S: Synonyms: Coronavirus della SARS Gene S di SARS-CoV-2 (COVID-19) Genetica molecolare Microbiologia Mutazione del gene S di SARS coronavirus 2; |
| nl-NL | Dutch (Netherlands) | SARS-CoV-2 S-genmutatie: Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Mutacja genu S SARS-CoV-2: Synonyms: diagnostyka molekularna Koronawirus |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 S 基因突变: Synonyms: 2019 新型冠状病毒; |
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
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) klad: |
| de-DE | German (Germany) | SARS-Coronavirus 2 Klade: |
| el-GR | Greek (Greece) | Κλάδος κορωνοϊού SARS 2: Synonyms: MICRO Nom Pt Type XXX Κλάδος κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Μοριακή γενετική |
| es-ES | Spanish (Spain) | Clado de SARS-CoV-2 (COVID-19): |
| es-MX | Spanish (Mexico) | SARS coronavirus 2 clado: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 clade: |
| it-IT | Italian (Italy) | SARS coronavirus 2 clade: 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: Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Klad SARS-CoV-2: Synonyms: diagnostyka molekularna Koronawirus wynik kategorialny |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 进化枝: Synonyms: 2019 新型冠状病毒; |
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
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 Also known as Nigerian variant | 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 Also known as WHO Alpha variant, and UK variant | 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 Also known as WHO Beta variant, GH/501Y.V2, and South Africa variant | LA32553-2 | ||
| SARS-CoV-2 P.1 lineage Also known as WHO gamma lineage, and Brazil variant | LA32555-7 | ||
| SARS-CoV-2 B.1.617.2 lineage Also known as WHO Delta variant | 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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) linie: |
| de-DE | German (Germany) | SARS-Coronavirus 2 Abstammungslinie: |
| el-GR | Greek (Greece) | Γενεαλογική σειρά κορωνοϊού SARS 2: Synonyms: MICRO Nom Prid Pt XXX Γενεαλογική σειρά κορωνοϊού SARS 2 Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Μοριακή γενετική |
| es-ES | Spanish (Spain) | Linaje de SARS-CoV-2 (COVID-19): |
| es-MX | Spanish (Mexico) | Linaje del coronavirus 2 del SARS: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 lignée: |
| it-IT | Italian (Italy) | SARS coronavirus 2, lignaggio: 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: Synonyms: molgen SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | SARS koronawirus linia genetyczna: Synonyms: diagnostyka molekularna Koronawirus Linia genetyczna SARS-CoV-2 wynik kategorialny |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 谱系: Synonyms: 2019 新型冠状病毒; |
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
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) 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 |
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) varianta: |
| de-AT | German (Austria) | Synonyms: SARS-CoV-2 Mutationsscreening ql. /SM |
| de-DE | German (Germany) | SARS-Coronavirus 2-Variante: |
| el-GR | Greek (Greece) | Παραλλαγή κορωνοϊού SARS 2: Synonyms: MICRO Nom Pt Type XXX Αλληλούχιση Κορωνοϊός Κορωνοϊός SARS Κορωνοϊός SARS 2 Παραλλαγή κορωνοϊού SARS 2 |
| es-ES | Spanish (Spain) | Variante del SARS-CoV-2 (COVID-19): |
| es-MX | Spanish (Mexico) | Variante del coronavirus 2 del SARS: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 variant: |
| fr-CA | French (Canada) | Variants du SRAS Coronavirus 2: |
| it-IT | Italian (Italy) | SARS coronavirus 2, variante: 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: Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Wariant SARS-CoV-2: Synonyms: Koronawirus wynik kategorialny |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 变异: Synonyms: 2019 新型冠状病毒; |
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).
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 |
|---|---|---|
| cs-CZ | Czech (Czechia) | SARS-CoV-2 (COVID-19) interpretace varianty: |
| de-DE | German (Germany) | SARS-Coronavirus 2 Varianteninterpretation: |
| el-GR | Greek (Greece) | Ερμηνεία παραλλαγής κορωνοϊού SARS 2: Synonyms: Imp MICRO Nar Pt XXX 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): |
| es-MX | Spanish (Mexico) | Interpretación de la variante del coronavirus 2 del SARS: |
| fr-FR | French (France) | Coronavirus SARS-CoV-2 variant - Interprétation: |
| it-IT | Italian (Italy) | SARS coronavirus 2, interpretazione variante: 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: Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; |
| pl-PL | Polish (Poland) | Interpretacja wariantu SARS-CoV-2: Synonyms: Koronawirus |
| zh-CN | Chinese (China) | SARS 冠状病毒 2 变异解释: Synonyms: 2019 新型冠状病毒; |