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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T93","span":{"begin":60,"end":63},"obj":"Body_part"},{"id":"T94","span":{"begin":170,"end":173},"obj":"Body_part"},{"id":"T95","span":{"begin":209,"end":212},"obj":"Body_part"},{"id":"T96","span":{"begin":578,"end":581},"obj":"Body_part"},{"id":"T97","span":{"begin":692,"end":695},"obj":"Body_part"},{"id":"T98","span":{"begin":737,"end":740},"obj":"Body_part"},{"id":"T99","span":{"begin":1471,"end":1475},"obj":"Body_part"},{"id":"T100","span":{"begin":2417,"end":2420},"obj":"Body_part"},{"id":"T101","span":{"begin":2712,"end":2715},"obj":"Body_part"}],"attributes":[{"id":"A93","pred":"fma_id","subj":"T93","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A94","pred":"fma_id","subj":"T94","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A95","pred":"fma_id","subj":"T95","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A96","pred":"fma_id","subj":"T96","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A97","pred":"fma_id","subj":"T97","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A98","pred":"fma_id","subj":"T98","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A99","pred":"fma_id","subj":"T99","obj":"http://purl.org/sig/ont/fma/fma12520"},{"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":"Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection\nTo determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples. We assayed a total of 768 RNA samples obtained on different days (fig. S1). Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.\nFig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.\n(A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates. The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated. The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation. The 96-well plate shown in Fig. 2 is not included here. Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown. The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay. For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay. The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).\nTable 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).\nFig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.\nRT-LAMP\nCT Pos Neg Sum\nRT-qPCR Pos 0–25 51 0 51\n25–30 28 2 30\n30–35 4 16 20\n35–40 0 16 16\nNeg Neg 2 649 651\nSum 85 683 768 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)."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T60","span":{"begin":49,"end":57},"obj":"Disease"},{"id":"T61","span":{"begin":567,"end":575},"obj":"Disease"},{"id":"T62","span":{"begin":2333,"end":2335},"obj":"Disease"},{"id":"T63","span":{"begin":2406,"end":2414},"obj":"Disease"},{"id":"T64","span":{"begin":2701,"end":2709},"obj":"Disease"},{"id":"T65","span":{"begin":3059,"end":3061},"obj":"Disease"}],"attributes":[{"id":"A60","pred":"mondo_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A61","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"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":"Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection\nTo determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples. We assayed a total of 768 RNA samples obtained on different days (fig. S1). Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.\nFig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.\n(A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates. The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated. The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation. The 96-well plate shown in Fig. 2 is not included here. Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown. The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay. For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay. The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).\nTable 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).\nFig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.\nRT-LAMP\nCT Pos Neg Sum\nRT-qPCR Pos 0–25 51 0 51\n25–30 28 2 30\n30–35 4 16 20\n35–40 0 16 16\nNeg Neg 2 649 651\nSum 85 683 768 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)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T53","span":{"begin":1892,"end":1894},"obj":"Chemical"},{"id":"T54","span":{"begin":2030,"end":2032},"obj":"Chemical"},{"id":"T55","span":{"begin":2896,"end":2903},"obj":"Chemical"},{"id":"T56","span":{"begin":3318,"end":3320},"obj":"Chemical"}],"attributes":[{"id":"A53","pred":"chebi_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A54","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"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":"Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection\nTo determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples. We assayed a total of 768 RNA samples obtained on different days (fig. S1). Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.\nFig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.\n(A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates. The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated. The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation. The 96-well plate shown in Fig. 2 is not included here. Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown. The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay. For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay. The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).\nTable 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).\nFig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.\nRT-LAMP\nCT Pos Neg Sum\nRT-qPCR Pos 0–25 51 0 51\n25–30 28 2 30\n30–35 4 16 20\n35–40 0 16 16\nNeg Neg 2 649 651\nSum 85 683 768 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)."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"191","span":{"begin":49,"end":59},"obj":"Species"},{"id":"193","span":{"begin":437,"end":451},"obj":"Gene"},{"id":"195","span":{"begin":567,"end":577},"obj":"Species"},{"id":"197","span":{"begin":1836,"end":1842},"obj":"Disease"},{"id":"203","span":{"begin":3000,"end":3014},"obj":"Gene"},{"id":"204","span":{"begin":2406,"end":2416},"obj":"Species"},{"id":"205","span":{"begin":2701,"end":2711},"obj":"Species"},{"id":"206","span":{"begin":3133,"end":3139},"obj":"Disease"},{"id":"207","span":{"begin":3250,"end":3256},"obj":"Disease"}],"attributes":[{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"Tax:2697049"},{"id":"A195","pred":"tao:has_database_id","subj":"195","obj":"Tax:2697049"},{"id":"A197","pred":"tao:has_database_id","subj":"197","obj":"MESH:D006527"},{"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":"Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection\nTo determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples. We assayed a total of 768 RNA samples obtained on different days (fig. S1). Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.\nFig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.\n(A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates. The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated. The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation. The 96-well plate shown in Fig. 2 is not included here. Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown. The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay. For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay. The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).\nTable 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).\nFig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.\nRT-LAMP\nCT Pos Neg Sum\nRT-qPCR Pos 0–25 51 0 51\n25–30 28 2 30\n30–35 4 16 20\n35–40 0 16 16\nNeg Neg 2 649 651\nSum 85 683 768 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)."}

LitCovid-PD-GO-BP

LitCovid-sentences