PMC:7574920 / 8028-9446 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T43","span":{"begin":605,"end":608},"obj":"Body_part"},{"id":"T44","span":{"begin":621,"end":624},"obj":"Body_part"},{"id":"T45","span":{"begin":845,"end":848},"obj":"Body_part"},{"id":"T46","span":{"begin":999,"end":1002},"obj":"Body_part"},{"id":"T47","span":{"begin":1043,"end":1046},"obj":"Body_part"}],"attributes":[{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T40","span":{"begin":457,"end":465},"obj":"Disease"},{"id":"T41","span":{"begin":594,"end":602},"obj":"Disease"},{"id":"T42","span":{"begin":717,"end":725},"obj":"Disease"},{"id":"T43","span":{"begin":834,"end":842},"obj":"Disease"}],"attributes":[{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A42","pred":"mondo_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T80","span":{"begin":89,"end":90},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T81","span":{"begin":190,"end":191},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T82","span":{"begin":509,"end":515},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T83","span":{"begin":551,"end":552},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T84","span":{"begin":706,"end":712},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T85","span":{"begin":849,"end":856},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T86","span":{"begin":875,"end":877},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T87","span":{"begin":898,"end":899},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T88","span":{"begin":1022,"end":1028},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T89","span":{"begin":1060,"end":1061},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T90","span":{"begin":1200,"end":1201},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-PubTator","denotations":[{"id":"118","span":{"begin":594,"end":604},"obj":"Species"},{"id":"119","span":{"begin":834,"end":844},"obj":"Species"},{"id":"120","span":{"begin":457,"end":465},"obj":"Disease"},{"id":"121","span":{"begin":717,"end":725},"obj":"Disease"}],"attributes":[{"id":"A118","pred":"tao:has_database_id","subj":"118","obj":"Tax:2697049"},{"id":"A119","pred":"tao:has_database_id","subj":"119","obj":"Tax:2697049"},{"id":"A120","pred":"tao:has_database_id","subj":"120","obj":"MESH:C000657245"},{"id":"A121","pred":"tao:has_database_id","subj":"121","obj":"MESH:C000657245"}],"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 performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T45","span":{"begin":22,"end":24},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T46","span":{"begin":566,"end":568},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T47","span":{"begin":860,"end":862},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T48","span":{"begin":908,"end":910},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T49","span":{"begin":1167,"end":1169},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T50","span":{"begin":1353,"end":1355},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":1254,"end":1257},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/AN0083"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}

{"project":"LitCovid-sentences","denotations":[{"id":"T53","span":{"begin":0,"end":280},"obj":"Sentence"},{"id":"T54","span":{"begin":281,"end":426},"obj":"Sentence"},{"id":"T55","span":{"begin":427,"end":879},"obj":"Sentence"},{"id":"T56","span":{"begin":880,"end":1018},"obj":"Sentence"},{"id":"T57","span":{"begin":1019,"end":1181},"obj":"Sentence"},{"id":"T58","span":{"begin":1182,"end":1418},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C. For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1). We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step. We tested \u003e700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay. We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run."}