PMC:7574920 / 26132-27232 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T114","span":{"begin":182,"end":185},"obj":"Body_part"},{"id":"T115","span":{"begin":353,"end":356},"obj":"Body_part"},{"id":"T116","span":{"begin":447,"end":460},"obj":"Body_part"},{"id":"T117","span":{"begin":447,"end":450},"obj":"Body_part"},{"id":"T118","span":{"begin":481,"end":485},"obj":"Body_part"},{"id":"T119","span":{"begin":698,"end":701},"obj":"Body_part"},{"id":"T120","span":{"begin":817,"end":820},"obj":"Body_part"},{"id":"T121","span":{"begin":1054,"end":1057},"obj":"Body_part"}],"attributes":[{"id":"A114","pred":"fma_id","subj":"T114","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A116","pred":"fma_id","subj":"T116","obj":"http://purl.org/sig/ont/fma/fma84126"},{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A120","pred":"fma_id","subj":"T120","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A121","pred":"fma_id","subj":"T121","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T67","span":{"begin":468,"end":476},"obj":"Disease"},{"id":"T68","span":{"begin":509,"end":517},"obj":"Disease"},{"id":"T69","span":{"begin":1043,"end":1051},"obj":"Disease"}],"attributes":[{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T231","span":{"begin":45,"end":47},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T232","span":{"begin":76,"end":78},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T233","span":{"begin":107,"end":114},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T234","span":{"begin":174,"end":175},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T235","span":{"begin":260,"end":264},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T236","span":{"begin":481,"end":485},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T237","span":{"begin":548,"end":554},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T238","span":{"begin":636,"end":641},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T239","span":{"begin":728,"end":733},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T240","span":{"begin":767,"end":769},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T241","span":{"begin":821,"end":828},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T242","span":{"begin":841,"end":846},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T63","span":{"begin":451,"end":460},"obj":"Chemical"},{"id":"T64","span":{"begin":607,"end":616},"obj":"Chemical"}],"attributes":[{"id":"A63","pred":"chebi_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A64","pred":"chebi_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/CHEBI_27780"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-PubTator","denotations":[{"id":"217","span":{"begin":479,"end":480},"obj":"Gene"},{"id":"218","span":{"begin":468,"end":478},"obj":"Species"},{"id":"219","span":{"begin":1043,"end":1053},"obj":"Species"},{"id":"220","span":{"begin":509,"end":517},"obj":"Disease"},{"id":"221","span":{"begin":1079,"end":1087},"obj":"Disease"}],"attributes":[{"id":"A217","pred":"tao:has_database_id","subj":"217","obj":"Gene:43740575"},{"id":"A218","pred":"tao:has_database_id","subj":"218","obj":"Tax:2697049"},{"id":"A219","pred":"tao:has_database_id","subj":"219","obj":"Tax:2697049"},{"id":"A220","pred":"tao:has_database_id","subj":"220","obj":"MESH:C000657245"},{"id":"A221","pred":"tao:has_database_id","subj":"221","obj":"MESH:D007239"}],"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":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T153","span":{"begin":36,"end":38},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T154","span":{"begin":56,"end":58},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T155","span":{"begin":235,"end":237},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T156","span":{"begin":296,"end":298},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T157","span":{"begin":900,"end":902},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}

{"project":"LitCovid-sentences","denotations":[{"id":"T191","span":{"begin":0,"end":218},"obj":"Sentence"},{"id":"T192","span":{"begin":219,"end":411},"obj":"Sentence"},{"id":"T193","span":{"begin":412,"end":544},"obj":"Sentence"},{"id":"T194","span":{"begin":545,"end":741},"obj":"Sentence"},{"id":"T195","span":{"begin":742,"end":771},"obj":"Sentence"},{"id":"T196","span":{"begin":772,"end":1100},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Several reports have indicated that RT-qPCR (18–20) and RT-LAMP assays (21, 22) are compatible with direct testing of nasopharyngeal and oropharyngeal swab specimens without a prior RNA purification or extraction step. To establish an RT-LAMP assay that could test unprocessed specimens (swab–to–RT-LAMP assay), we first assessed the stability of naked RNA in swab specimens that were collected in Amies medium. We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects. We tested different conditions, particularly the influence of detergent (to inactivate the virus) and heat (to denature the capsid and release the viral RNA as well as inactivate the virus) (figs. S6 and S7, and data file S1). Consistent with previous reports about other RNA viruses (23–25) and tests using heat inactivation of swab specimens for direct RT-qPCR assays (26), these experiments established that native swab specimens and heat-treated swab specimens were compatible for detection of SARS-CoV-2 RNA in swab samples from infected individuals."}