PMC:7574920 / 6818-8027 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T34","span":{"begin":10,"end":13},"obj":"Body_part"},{"id":"T35","span":{"begin":451,"end":454},"obj":"Body_part"},{"id":"T36","span":{"begin":555,"end":558},"obj":"Body_part"},{"id":"T37","span":{"begin":611,"end":614},"obj":"Body_part"},{"id":"T38","span":{"begin":715,"end":718},"obj":"Body_part"},{"id":"T39","span":{"begin":788,"end":801},"obj":"Body_part"},{"id":"T40","span":{"begin":788,"end":791},"obj":"Body_part"},{"id":"T41","span":{"begin":848,"end":851},"obj":"Body_part"},{"id":"T42","span":{"begin":938,"end":941},"obj":"Body_part"}],"attributes":[{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma84126"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma74412"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T37","span":{"begin":472,"end":481},"obj":"Disease"},{"id":"T38","span":{"begin":600,"end":608},"obj":"Disease"},{"id":"T39","span":{"begin":837,"end":845},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A39","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T69","span":{"begin":110,"end":111},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T70","span":{"begin":168,"end":169},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T71","span":{"begin":267,"end":268},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T72","span":{"begin":455,"end":462},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T73","span":{"begin":482,"end":487},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T74","span":{"begin":738,"end":739},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T75","span":{"begin":853,"end":854},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T76","span":{"begin":876,"end":881},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T77","span":{"begin":1047,"end":1048},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T78","span":{"begin":1142,"end":1143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T79","span":{"begin":1196,"end":1200},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T24","span":{"begin":10,"end":13},"obj":"Chemical"},{"id":"T25","span":{"begin":115,"end":124},"obj":"Chemical"},{"id":"T26","span":{"begin":132,"end":142},"obj":"Chemical"},{"id":"T27","span":{"begin":132,"end":138},"obj":"Chemical"},{"id":"T28","span":{"begin":555,"end":558},"obj":"Chemical"},{"id":"T29","span":{"begin":792,"end":801},"obj":"Chemical"},{"id":"T30","span":{"begin":938,"end":941},"obj":"Chemical"}],"attributes":[{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_47867"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_31991"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_15882"},{"id":"A28","pred":"chebi_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-PubTator","denotations":[{"id":"108","span":{"begin":235,"end":237},"obj":"Gene"},{"id":"109","span":{"begin":112,"end":114},"obj":"Gene"},{"id":"110","span":{"begin":472,"end":487},"obj":"Species"},{"id":"111","span":{"begin":600,"end":610},"obj":"Species"},{"id":"112","span":{"begin":837,"end":847},"obj":"Species"},{"id":"113","span":{"begin":132,"end":142},"obj":"Chemical"}],"attributes":[{"id":"A108","pred":"tao:has_database_id","subj":"108","obj":"Gene:5053"},{"id":"A109","pred":"tao:has_database_id","subj":"109","obj":"Gene:5053"},{"id":"A110","pred":"tao:has_database_id","subj":"110","obj":"Tax:11309"},{"id":"A111","pred":"tao:has_database_id","subj":"111","obj":"Tax:2697049"},{"id":"A112","pred":"tao:has_database_id","subj":"112","obj":"Tax:2697049"},{"id":"A113","pred":"tao:has_database_id","subj":"113","obj":"MESH:D010637"}],"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":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T41","span":{"begin":28,"end":30},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T42","span":{"begin":383,"end":385},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T43","span":{"begin":555,"end":572},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T44","span":{"begin":938,"end":955},"obj":"http://purl.obolibrary.org/obo/GO_0006277"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}

{"project":"LitCovid-sentences","denotations":[{"id":"T45","span":{"begin":0,"end":83},"obj":"Sentence"},{"id":"T46","span":{"begin":84,"end":198},"obj":"Sentence"},{"id":"T47","span":{"begin":199,"end":370},"obj":"Sentence"},{"id":"T48","span":{"begin":371,"end":492},"obj":"Sentence"},{"id":"T49","span":{"begin":493,"end":615},"obj":"Sentence"},{"id":"T50","span":{"begin":616,"end":815},"obj":"Sentence"},{"id":"T51","span":{"begin":816,"end":1068},"obj":"Sentence"},{"id":"T52","span":{"begin":1069,"end":1209},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To detect DNA production in RT-LAMP assays, various approaches have been described. One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment. As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8). Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9). Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA. The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction. For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format. Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples."}