PMC:7574920 / 1223-2876 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T8","span":{"begin":297,"end":300},"obj":"Body_part"},{"id":"T9","span":{"begin":740,"end":743},"obj":"Body_part"},{"id":"T10","span":{"begin":782,"end":786},"obj":"Body_part"},{"id":"T11","span":{"begin":827,"end":830},"obj":"Body_part"},{"id":"T12","span":{"begin":1035,"end":1038},"obj":"Body_part"},{"id":"T13","span":{"begin":1160,"end":1163},"obj":"Body_part"},{"id":"T14","span":{"begin":1348,"end":1351},"obj":"Body_part"}],"attributes":[{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T8","span":{"begin":4,"end":28},"obj":"Disease"},{"id":"T9","span":{"begin":30,"end":38},"obj":"Disease"},{"id":"T10","span":{"begin":63,"end":71},"obj":"Disease"},{"id":"T11","span":{"begin":75,"end":122},"obj":"Disease"},{"id":"T12","span":{"begin":75,"end":108},"obj":"Disease"},{"id":"T13","span":{"begin":207,"end":215},"obj":"Disease"},{"id":"T14","span":{"begin":218,"end":228},"obj":"Disease"},{"id":"T15","span":{"begin":723,"end":731},"obj":"Disease"},{"id":"T16","span":{"begin":927,"end":935},"obj":"Disease"},{"id":"T17","span":{"begin":1018,"end":1026},"obj":"Disease"},{"id":"T18","span":{"begin":1149,"end":1157},"obj":"Disease"}],"attributes":[{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T14","span":{"begin":139,"end":140},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T15","span":{"begin":178,"end":183},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T16","span":{"begin":243,"end":248},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T17","span":{"begin":440,"end":447},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T18","span":{"begin":573,"end":574},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T19","span":{"begin":641,"end":656},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T20","span":{"begin":667,"end":673},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T21","span":{"begin":674,"end":675},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T22","span":{"begin":750,"end":751},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T23","span":{"begin":782,"end":786},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T24","span":{"begin":791,"end":797},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T25","span":{"begin":916,"end":922},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T26","span":{"begin":1075,"end":1076},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T27","span":{"begin":1226,"end":1227},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T28","span":{"begin":1253,"end":1254},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T29","span":{"begin":1295,"end":1296},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T30","span":{"begin":1340,"end":1341},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T31","span":{"begin":1510,"end":1511},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T32","span":{"begin":1565,"end":1566},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}

{"project":"LitCovid-PubTator","denotations":[{"id":"31","span":{"begin":780,"end":781},"obj":"Gene"},{"id":"32","span":{"begin":63,"end":73},"obj":"Species"},{"id":"33","span":{"begin":75,"end":122},"obj":"Species"},{"id":"34","span":{"begin":124,"end":135},"obj":"Species"},{"id":"35","span":{"begin":723,"end":733},"obj":"Species"},{"id":"36","span":{"begin":1018,"end":1028},"obj":"Species"},{"id":"37","span":{"begin":1149,"end":1159},"obj":"Species"},{"id":"38","span":{"begin":4,"end":28},"obj":"Disease"},{"id":"39","span":{"begin":30,"end":38},"obj":"Disease"},{"id":"40","span":{"begin":207,"end":228},"obj":"Disease"},{"id":"41","span":{"begin":927,"end":935},"obj":"Disease"}],"attributes":[{"id":"A31","pred":"tao:has_database_id","subj":"31","obj":"Gene:43740575"},{"id":"A32","pred":"tao:has_database_id","subj":"32","obj":"Tax:2697049"},{"id":"A33","pred":"tao:has_database_id","subj":"33","obj":"Tax:2697049"},{"id":"A34","pred":"tao:has_database_id","subj":"34","obj":"Tax:11118"},{"id":"A35","pred":"tao:has_database_id","subj":"35","obj":"Tax:2697049"},{"id":"A36","pred":"tao:has_database_id","subj":"36","obj":"Tax:2697049"},{"id":"A37","pred":"tao:has_database_id","subj":"37","obj":"Tax:2697049"},{"id":"A38","pred":"tao:has_database_id","subj":"38","obj":"MESH:C000657245"},{"id":"A39","pred":"tao:has_database_id","subj":"39","obj":"MESH:C000657245"},{"id":"A40","pred":"tao:has_database_id","subj":"40","obj":"MESH:C000657245"},{"id":"A41","pred":"tao:has_database_id","subj":"41","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 coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T10","span":{"begin":310,"end":331},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T11","span":{"begin":318,"end":331},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T12","span":{"begin":372,"end":374},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T13","span":{"begin":469,"end":471},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T14","span":{"begin":512,"end":514},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T15","span":{"begin":536,"end":538},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T16","span":{"begin":686,"end":688},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T17","span":{"begin":802,"end":804},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T18","span":{"begin":990,"end":992},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T19","span":{"begin":1055,"end":1057},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T20","span":{"begin":1117,"end":1119},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T21","span":{"begin":1172,"end":1174},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T22","span":{"begin":1305,"end":1307},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T23","span":{"begin":1469,"end":1471},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T24","span":{"begin":1635,"end":1637},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}

{"project":"LitCovid-sentences","denotations":[{"id":"T11","span":{"begin":0,"end":171},"obj":"Sentence"},{"id":"T12","span":{"begin":172,"end":269},"obj":"Sentence"},{"id":"T13","span":{"begin":270,"end":456},"obj":"Sentence"},{"id":"T14","span":{"begin":457,"end":657},"obj":"Sentence"},{"id":"T15","span":{"begin":658,"end":787},"obj":"Sentence"},{"id":"T16","span":{"begin":788,"end":936},"obj":"Sentence"},{"id":"T17","span":{"begin":937,"end":1039},"obj":"Sentence"},{"id":"T18","span":{"begin":1040,"end":1276},"obj":"Sentence"},{"id":"T19","span":{"begin":1277,"end":1483},"obj":"Sentence"},{"id":"T20","span":{"begin":1484,"end":1653},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT \u003c 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions."}