PMC:7574920 / 25756-27232 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T111","span":{"begin":32,"end":35},"obj":"Body_part"},{"id":"T112","span":{"begin":46,"end":49},"obj":"Body_part"},{"id":"T113","span":{"begin":203,"end":206},"obj":"Body_part"},{"id":"T114","span":{"begin":558,"end":561},"obj":"Body_part"},{"id":"T115","span":{"begin":729,"end":732},"obj":"Body_part"},{"id":"T116","span":{"begin":823,"end":836},"obj":"Body_part"},{"id":"T117","span":{"begin":823,"end":826},"obj":"Body_part"},{"id":"T118","span":{"begin":857,"end":861},"obj":"Body_part"},{"id":"T119","span":{"begin":1074,"end":1077},"obj":"Body_part"},{"id":"T120","span":{"begin":1193,"end":1196},"obj":"Body_part"},{"id":"T121","span":{"begin":1430,"end":1433},"obj":"Body_part"}],"attributes":[{"id":"A111","pred":"fma_id","subj":"T111","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A112","pred":"fma_id","subj":"T112","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A113","pred":"fma_id","subj":"T113","obj":"http://purl.org/sig/ont/fma/fma67095"},{"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":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":844,"end":852},"obj":"Disease"},{"id":"T68","span":{"begin":885,"end":893},"obj":"Disease"},{"id":"T69","span":{"begin":1419,"end":1427},"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":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":"T229","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T230","span":{"begin":150,"end":151},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T231","span":{"begin":421,"end":423},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T232","span":{"begin":452,"end":454},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T233","span":{"begin":483,"end":490},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T234","span":{"begin":550,"end":551},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T235","span":{"begin":636,"end":640},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T236","span":{"begin":857,"end":861},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T237","span":{"begin":924,"end":930},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T238","span":{"begin":1012,"end":1017},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T239","span":{"begin":1104,"end":1109},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T240","span":{"begin":1143,"end":1145},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T241","span":{"begin":1197,"end":1204},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T242","span":{"begin":1217,"end":1222},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":"T61","span":{"begin":102,"end":110},"obj":"Chemical"},{"id":"T62","span":{"begin":230,"end":236},"obj":"Chemical"},{"id":"T63","span":{"begin":827,"end":836},"obj":"Chemical"},{"id":"T64","span":{"begin":983,"end":992},"obj":"Chemical"}],"attributes":[{"id":"A61","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_33893"},{"id":"A62","pred":"chebi_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/CHEBI_30563"},{"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":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":"211","span":{"begin":230,"end":240},"obj":"Chemical"},{"id":"217","span":{"begin":855,"end":856},"obj":"Gene"},{"id":"218","span":{"begin":844,"end":854},"obj":"Species"},{"id":"219","span":{"begin":1419,"end":1429},"obj":"Species"},{"id":"220","span":{"begin":885,"end":893},"obj":"Disease"},{"id":"221","span":{"begin":1455,"end":1463},"obj":"Disease"}],"attributes":[{"id":"A211","pred":"tao:has_database_id","subj":"211","obj":"MESH:D058428"},{"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":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":"T152","span":{"begin":10,"end":12},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T153","span":{"begin":412,"end":414},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T154","span":{"begin":432,"end":434},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T155","span":{"begin":611,"end":613},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T156","span":{"begin":672,"end":674},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T157","span":{"begin":1276,"end":1278},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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":"T188","span":{"begin":0,"end":45},"obj":"Sentence"},{"id":"T189","span":{"begin":46,"end":161},"obj":"Sentence"},{"id":"T190","span":{"begin":162,"end":375},"obj":"Sentence"},{"id":"T191","span":{"begin":376,"end":594},"obj":"Sentence"},{"id":"T192","span":{"begin":595,"end":787},"obj":"Sentence"},{"id":"T193","span":{"begin":788,"end":920},"obj":"Sentence"},{"id":"T194","span":{"begin":921,"end":1117},"obj":"Sentence"},{"id":"T195","span":{"begin":1118,"end":1147},"obj":"Sentence"},{"id":"T196","span":{"begin":1148,"end":1476},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A swab–to–RT-LAMP assay without RNA isolation\nRNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic. Alternative, noncommercial solutions for RNA isolation, e.g., using silica gel matrix or magnetic beads, require specialized knowledge and cannot be implemented easily for point-of-care or decentralized screening.\nSeveral 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."}