PMC:7574920 / 19420-20486 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T100","span":{"begin":161,"end":164},"obj":"Body_part"},{"id":"T101","span":{"begin":456,"end":459},"obj":"Body_part"}],"attributes":[{"id":"A100","pred":"fma_id","subj":"T100","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A101","pred":"fma_id","subj":"T101","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T62","span":{"begin":77,"end":79},"obj":"Disease"},{"id":"T63","span":{"begin":150,"end":158},"obj":"Disease"},{"id":"T64","span":{"begin":445,"end":453},"obj":"Disease"},{"id":"T65","span":{"begin":803,"end":805},"obj":"Disease"}],"attributes":[{"id":"A62","pred":"mondo_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A64","pred":"mondo_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A65","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T194","span":{"begin":61,"end":62},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T195","span":{"begin":90,"end":91},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T196","span":{"begin":206,"end":207},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T197","span":{"begin":361,"end":363},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T198","span":{"begin":488,"end":489},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T199","span":{"begin":861,"end":869},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T200","span":{"begin":1062,"end":1064},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T201","span":{"begin":1062,"end":1064},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T55","span":{"begin":640,"end":647},"obj":"Chemical"},{"id":"T56","span":{"begin":1062,"end":1064},"obj":"Chemical"}],"attributes":[{"id":"A55","pred":"chebi_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/CHEBI_33893"},{"id":"A56","pred":"chebi_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"203","span":{"begin":744,"end":758},"obj":"Gene"},{"id":"204","span":{"begin":150,"end":160},"obj":"Species"},{"id":"205","span":{"begin":445,"end":455},"obj":"Species"},{"id":"206","span":{"begin":877,"end":883},"obj":"Disease"},{"id":"207","span":{"begin":994,"end":1000},"obj":"Disease"}],"attributes":[{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"Tax:2697049"},{"id":"A205","pred":"tao:has_database_id","subj":"205","obj":"Tax:2697049"},{"id":"A206","pred":"tao:has_database_id","subj":"206","obj":"MESH:D006527"},{"id":"A207","pred":"tao:has_database_id","subj":"207","obj":"MESH:D006527"}],"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":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T114","span":{"begin":176,"end":178},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T115","span":{"begin":239,"end":241},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T116","span":{"begin":414,"end":416},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T117","span":{"begin":671,"end":673},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T118","span":{"begin":724,"end":726},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T119","span":{"begin":853,"end":855},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T120","span":{"begin":975,"end":977},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T131","span":{"begin":176,"end":375},"obj":"Sentence"},{"id":"T132","span":{"begin":376,"end":498},"obj":"Sentence"},{"id":"T133","span":{"begin":499,"end":657},"obj":"Sentence"},{"id":"T134","span":{"begin":658,"end":821},"obj":"Sentence"},{"id":"T135","span":{"begin":822,"end":910},"obj":"Sentence"},{"id":"T136","span":{"begin":911,"end":1027},"obj":"Sentence"},{"id":"T137","span":{"begin":1028,"end":1066},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The consistency of the results during the analysis confirmed a threshold of ΔOD \u003e +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A). RT-qPCR–positive samples with a CT \u003c 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B). This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT \u003c 30. We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling. We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3. The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval: 98.9 to 99.9%), and the sensitivity for samples with CT \u003c 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval: 91.4 to 99.3%) (Fig. 3B and table S2)."}