PMC:6988269 / 7846-8725 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/6988269","sourcedb":"PMC","sourceid":"6988269","source_url":"https://www.ncbi.nlm.nih.gov/pmc/6988269","text":"Protocol options and application notes\nLaboratories participating in the evaluation used the TaqMan Fast Virus 1-Step Master Mix (Thermo Fisher) with the same oligonucleotide concentrations and cycling conditions. The QIAGEN One-Step RT-PCR Kit was also tested and found to be compatible.\nThe intended cross-reactivity of all assays with viral RNA of SARS-CoV allows us to use the assays without having to rely on external sources of specific 2019-nCoV RNA.\nFor a routine workflow, we recommend the E gene assay as the first-line screening tool, followed by confirmatory testing with the RdRp gene assay. Application of the RdRp gene assay with dual colour technology can discriminate 2019-nCoV (both probes positive) from SARS-CoV RNA if the latter is used as positive control. Alternatively, laboratories may choose to run the RdRp assay with only the 2019-nCoV-specific probe.","divisions":[{"label":"title","span":{"begin":0,"end":38}},{"label":"p","span":{"begin":39,"end":288}},{"label":"p","span":{"begin":289,"end":457}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T20","span":{"begin":344,"end":347},"obj":"Body_part"},{"id":"T21","span":{"begin":453,"end":456},"obj":"Body_part"},{"id":"T22","span":{"begin":501,"end":505},"obj":"Body_part"},{"id":"T23","span":{"begin":593,"end":597},"obj":"Body_part"},{"id":"T24","span":{"begin":629,"end":633},"obj":"Body_part"},{"id":"T25","span":{"begin":732,"end":735},"obj":"Body_part"}],"attributes":[{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma67095"},{"subj":"T20","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T22","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T23","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T24","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T25","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T18","span":{"begin":351,"end":359},"obj":"Disease"},{"id":"T19","span":{"begin":351,"end":355},"obj":"Disease"},{"id":"T20","span":{"begin":723,"end":731},"obj":"Disease"},{"id":"T21","span":{"begin":723,"end":727},"obj":"Disease"}],"attributes":[{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T18","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T19","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T20","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T70","span":{"begin":105,"end":110},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T71","span":{"begin":254,"end":260},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T72","span":{"begin":462,"end":463},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T73","span":{"begin":501,"end":505},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T74","span":{"begin":571,"end":578},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T75","span":{"begin":593,"end":597},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T76","span":{"begin":629,"end":633},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"attributes":[{"subj":"T70","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T75","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T76","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T26","span":{"begin":21,"end":32},"obj":"Chemical"},{"id":"T27","span":{"begin":159,"end":174},"obj":"Chemical"},{"id":"T28","span":{"begin":873,"end":878},"obj":"Chemical"}],"attributes":[{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_33232"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_7754"},{"id":"A28","pred":"chebi_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"subj":"T26","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T27","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T28","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T63","span":{"begin":0,"end":38},"obj":"Sentence"},{"id":"T64","span":{"begin":39,"end":213},"obj":"Sentence"},{"id":"T65","span":{"begin":214,"end":288},"obj":"Sentence"},{"id":"T66","span":{"begin":289,"end":457},"obj":"Sentence"},{"id":"T67","span":{"begin":458,"end":604},"obj":"Sentence"},{"id":"T68","span":{"begin":605,"end":778},"obj":"Sentence"},{"id":"T69","span":{"begin":779,"end":879},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T63","pred":"source","obj":"LitCovid-sentences"},{"subj":"T64","pred":"source","obj":"LitCovid-sentences"},{"subj":"T65","pred":"source","obj":"LitCovid-sentences"},{"subj":"T66","pred":"source","obj":"LitCovid-sentences"},{"subj":"T67","pred":"source","obj":"LitCovid-sentences"},{"subj":"T68","pred":"source","obj":"LitCovid-sentences"},{"subj":"T69","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"141","span":{"begin":125,"end":128},"obj":"Gene"},{"id":"142","span":{"begin":241,"end":244},"obj":"Gene"},{"id":"143","span":{"begin":159,"end":174},"obj":"Chemical"},{"id":"146","span":{"begin":351,"end":359},"obj":"Species"},{"id":"147","span":{"begin":443,"end":452},"obj":"Species"},{"id":"154","span":{"begin":588,"end":592},"obj":"Gene"},{"id":"155","span":{"begin":624,"end":628},"obj":"Gene"},{"id":"156","span":{"begin":829,"end":833},"obj":"Gene"},{"id":"157","span":{"begin":685,"end":694},"obj":"Species"},{"id":"158","span":{"begin":723,"end":731},"obj":"Species"},{"id":"159","span":{"begin":854,"end":863},"obj":"Species"}],"attributes":[{"id":"A141","pred":"tao:has_database_id","subj":"141","obj":"Gene:83881"},{"id":"A142","pred":"tao:has_database_id","subj":"142","obj":"Gene:3815"},{"id":"A143","pred":"tao:has_database_id","subj":"143","obj":"MESH:D009841"},{"id":"A146","pred":"tao:has_database_id","subj":"146","obj":"Tax:694009"},{"id":"A147","pred":"tao:has_database_id","subj":"147","obj":"Tax:2697049"},{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"Gene:43740578"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Gene:43740578"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"Gene:43740578"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"Tax:2697049"},{"id":"A158","pred":"tao:has_database_id","subj":"158","obj":"Tax:694009"},{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"Tax:2697049"},{"subj":"141","pred":"source","obj":"LitCovid-PubTator"},{"subj":"142","pred":"source","obj":"LitCovid-PubTator"},{"subj":"143","pred":"source","obj":"LitCovid-PubTator"},{"subj":"146","pred":"source","obj":"LitCovid-PubTator"},{"subj":"147","pred":"source","obj":"LitCovid-PubTator"},{"subj":"154","pred":"source","obj":"LitCovid-PubTator"},{"subj":"155","pred":"source","obj":"LitCovid-PubTator"},{"subj":"156","pred":"source","obj":"LitCovid-PubTator"},{"subj":"157","pred":"source","obj":"LitCovid-PubTator"},{"subj":"158","pred":"source","obj":"LitCovid-PubTator"},{"subj":"159","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#93d8ec","default":true},{"id":"LitCovid-PD-MONDO","color":"#ece593"},{"id":"LitCovid-PD-CLO","color":"#cb93ec"},{"id":"LitCovid-PD-CHEBI","color":"#93ecb1"},{"id":"LitCovid-sentences","color":"#ec9793"},{"id":"LitCovid-PubTator","color":"#93a8ec"}]}]}}