PMC:7574920 / 15869-16723 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T82","span":{"begin":182,"end":186},"obj":"Body_part"},{"id":"T83","span":{"begin":230,"end":234},"obj":"Body_part"},{"id":"T84","span":{"begin":363,"end":367},"obj":"Body_part"},{"id":"T85","span":{"begin":488,"end":492},"obj":"Body_part"},{"id":"T86","span":{"begin":499,"end":503},"obj":"Body_part"},{"id":"T87","span":{"begin":618,"end":622},"obj":"Body_part"},{"id":"T88","span":{"begin":662,"end":666},"obj":"Body_part"},{"id":"T89","span":{"begin":700,"end":703},"obj":"Body_part"},{"id":"T90","span":{"begin":809,"end":813},"obj":"Body_part"}],"attributes":[{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A84","pred":"fma_id","subj":"T84","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A85","pred":"fma_id","subj":"T85","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A86","pred":"fma_id","subj":"T86","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma74402"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T59","span":{"begin":689,"end":697},"obj":"Disease"}],"attributes":[{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T153","span":{"begin":155,"end":161},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T154","span":{"begin":182,"end":186},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T155","span":{"begin":201,"end":202},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T156","span":{"begin":230,"end":234},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T157","span":{"begin":363,"end":367},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T158","span":{"begin":392,"end":393},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T159","span":{"begin":428,"end":430},"obj":"http://purl.obolibrary.org/obo/CLO_0001000"},{"id":"T160","span":{"begin":488,"end":492},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T161","span":{"begin":499,"end":503},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T162","span":{"begin":541,"end":542},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T163","span":{"begin":618,"end":622},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T164","span":{"begin":662,"end":666},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T165","span":{"begin":809,"end":813},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"179","span":{"begin":830,"end":834},"obj":"Gene"},{"id":"180","span":{"begin":616,"end":617},"obj":"Gene"},{"id":"181","span":{"begin":361,"end":362},"obj":"Gene"},{"id":"182","span":{"begin":228,"end":229},"obj":"Gene"},{"id":"183","span":{"begin":689,"end":699},"obj":"Species"}],"attributes":[{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Gene:43740578"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Gene:43740575"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Gene:43740575"},{"id":"A182","pred":"tao:has_database_id","subj":"182","obj":"Gene:43740575"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"Tax:2697049"}],"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_"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T86","span":{"begin":120,"end":122},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T87","span":{"begin":210,"end":212},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T88","span":{"begin":309,"end":311},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T89","span":{"begin":707,"end":709},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T101","span":{"begin":0,"end":294},"obj":"Sentence"},{"id":"T102","span":{"begin":295,"end":442},"obj":"Sentence"},{"id":"T103","span":{"begin":443,"end":591},"obj":"Sentence"},{"id":"T104","span":{"begin":592,"end":715},"obj":"Sentence"},{"id":"T105","span":{"begin":716,"end":854},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15). When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A). Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B). This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR. Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16)."}