> top > docs > PMC:7574920 > spans > 2878-58709 > annotations

PMC:7574920 / 2878-58709 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T15 1331-1337 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T16 1543-1546 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 1632-1635 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 1893-1896 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 1934-1940 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T20 2036-2039 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 2045-2048 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T22 2081-2084 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T23 2210-2216 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T24 2872-2875 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 2978-2981 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 3019-3026 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T27 3202-3205 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T28 3312-3315 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T29 3606-3609 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T30 3641-3644 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T31 3659-3663 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T32 3735-3738 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T33 3776-3779 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 3950-3953 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T35 4391-4394 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T36 4495-4498 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T37 4551-4554 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38 4655-4658 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T39 4728-4741 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T40 4728-4731 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41 4788-4791 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T42 4878-4881 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T43 5755-5758 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T44 5771-5774 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 5995-5998 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T46 6149-6152 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T47 6193-6196 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T48 6662-6665 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T49 6696-6699 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T50 6772-6775 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T51 6780-6783 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 7267-7270 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T53 7390-7393 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T54 7448-7451 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T55 7479-7485 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T56 7515-7519 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T57 7647-7651 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 7685-7698 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T59 7685-7688 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T60 7731-7734 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 8187-8190 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 8306-8309 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T63 8361-8374 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T64 8361-8364 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T65 8395-8399 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T66 8894-8907 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T67 8894-8897 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T68 9010-9013 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T69 9203-9206 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T70 9274-9277 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T71 10117-10121 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T72 10167-10170 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T73 10334-10337 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T74 10779-10783 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T75 12364-12377 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T76 12364-12367 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T77 12608-12611 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T78 12767-12780 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T79 12767-12770 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T80 12927-12930 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81 12934-12937 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T82 13173-13177 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T83 13221-13225 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T84 13354-13358 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 13479-13483 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T86 13490-13494 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T87 13609-13613 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 13653-13657 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T89 13691-13694 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T90 13800-13804 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T91 13990-13994 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T92 14072-14076 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T93 14346-14349 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T94 14456-14459 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T95 14495-14498 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T96 14864-14867 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T97 14978-14981 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T98 15023-15026 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 15757-15761 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T100 16703-16706 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T101 16998-17001 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T102 18233-18236 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T103 18776-18779 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T104 19569-19573 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T105 19591-19595 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T106 19699-19702 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T107 20139-20143 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T108 20217-20221 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T109 20357-20363 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T110 20702-20705 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T111 22910-22913 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T112 22924-22927 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T113 23081-23084 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T114 23436-23439 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T115 23607-23610 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T116 23701-23714 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T117 23701-23704 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T118 23735-23739 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T119 23952-23955 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T120 24071-24074 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T121 24308-24311 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T122 25935-25938 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T123 27463-27466 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T124 28986-28990 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T125 29147-29151 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T126 29941-29944 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T127 30291-30295 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T128 30500-30503 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T129 30541-30544 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T130 30896-30899 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T131 31081-31085 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T132 31581-31588 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T133 31635-31641 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T134 31645-31650 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T135 31782-31788 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T136 31955-31961 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T137 32167-32170 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T138 32425-32433 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 32554-32557 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T140 32791-32794 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T141 33050-33053 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T142 33188-33191 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T143 33472-33475 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T144 33590-33593 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T145 34250-34253 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T146 34941-34944 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T147 35835-35838 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T148 35953-35956 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T149 36040-36044 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T150 37818-37821 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T151 38707-38714 Body_part denotes pharynx http://purl.org/sig/ont/fma/fma46688
T152 39078-39081 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T153 39758-39764 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T154 40119-40122 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T155 40126-40129 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T156 40256-40259 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T157 40716-40720 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472
T158 40745-40750 Body_part denotes mouth http://purl.org/sig/ont/fma/fma49184
T159 41018-41021 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T160 41025-41028 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T161 41288-41291 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T162 41295-41298 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T163 41363-41366 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T164 41410-41413 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T165 41429-41432 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T166 41579-41582 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T167 42643-42646 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T168 42745-42748 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T169 42952-42955 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T170 43001-43004 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T171 43253-43259 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T172 43608-43611 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T173 43702-43706 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T174 43819-43823 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T175 43891-43894 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T176 44016-44019 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T177 44157-44160 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T178 44261-44265 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T179 44297-44301 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T180 44302-44305 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T181 44499-44503 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T182 44751-44754 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T183 44782-44786 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T184 44877-44880 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T185 45747-45750 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T186 45821-45824 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T187 46009-46012 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T188 46537-46540 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T189 47827-47831 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T190 49853-49856 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T191 50525-50528 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T192 50924-50927 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T193 52633-52639 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T194 52731-52737 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T195 52874-52880 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T196 53426-53430 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T197 54731-54734 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 785-790 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 31081-31085 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T4 31635-31641 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 31645-31650 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T6 31782-31788 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T7 31955-31961 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T8 36140-36144 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T9 37023-37028 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T10 37514-37519 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T11 38707-38714 Body_part denotes pharynx http://purl.obolibrary.org/obo/UBERON_0006562
T12 39758-39764 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T13 40716-40720 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004
T14 40745-40750 Body_part denotes mouth http://purl.obolibrary.org/obo/UBERON_0000165
T15 44553-44558 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T19 17-41 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T20 43-51 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 77-85 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 89-136 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T23 89-122 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T24 327-335 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 495-503 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 506-515 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T27 585-593 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 662-671 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T29 1004-1013 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T30 1263-1271 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 1274-1283 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T32 1407-1415 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 1621-1629 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 1678-1686 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 2624-2632 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 2861-2869 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 4412-4421 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 4540-4548 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 4777-4785 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 5607-5615 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 5744-5752 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 5867-5875 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 5984-5992 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 6651-6659 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 6685-6693 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 7256-7264 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 7468-7476 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 8382-8390 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 8883-8891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 9537-9539 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T51 9759-9761 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T52 10766-10774 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 10903-10905 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T54 11062-11064 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T55 11123-11125 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T56 11337-11339 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T57 11822-11824 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T58 11908-11910 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T59 13680-13688 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 14335-14343 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 14853-14861 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 16619-16621 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T63 16692-16700 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 16987-16995 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 17345-17347 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T66 19688-19696 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 23722-23730 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 23763-23771 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T69 24297-24305 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 26175-26177 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T71 27512-27514 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T72 27995-27997 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T73 28433-28435 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T74 28578-28580 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T75 28954-28956 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T76 29066-29068 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T77 29809-29817 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 29820-29829 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 30489-30497 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 31045-31053 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 31306-31314 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 31317-31326 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 33725-33733 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 35255-35263 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 38167-38175 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 38178-38187 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 38343-38353 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T88 38383-38391 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T89 38469-38477 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 38480-38489 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 38584-38592 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T92 40108-40116 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 40212-40220 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T94 40326-40334 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T95 40337-40346 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T96 41001-41009 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 41277-41285 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 41352-41360 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 42381-42388 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T100 43236-43244 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 43681-43685 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T102 43798-43802 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T103 45655-45658 Disease denotes SBS http://purl.obolibrary.org/obo/MONDO_0011526
T104 48354-48356 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T105 52612-52620 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 53413-53421 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 158-159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 188-189 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35 308-309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 352-353 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 428-435 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T38 484-490 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T39 629-634 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T40 636-640 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T41 691-699 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T42 754-759 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 852-857 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T44 1052-1059 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T45 1083-1084 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 1115-1116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 1256-1262 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T48 1371-1376 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 1648-1655 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T50 1714-1717 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T51 1777-1781 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T52 1974-1975 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 2062-2063 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 2173-2174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 2183-2184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 2263-2264 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 2305-2312 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T58 2318-2319 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 2441-2442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 2576-2580 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T61 2811-2815 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T62 3172-3173 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 3200-3201 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 3249-3257 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T65 3336-3337 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 3462-3463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 3770-3771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 3800-3801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 4050-4051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 4108-4109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 4207-4208 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 4395-4402 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 4422-4427 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 4678-4679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 4793-4794 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 4816-4821 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T77 4987-4988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 5082-5083 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 5136-5140 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T80 5239-5240 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 5340-5341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 5659-5665 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T83 5701-5702 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 5856-5862 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T85 5999-6006 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T86 6025-6027 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T87 6048-6049 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 6172-6178 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T89 6210-6211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 6350-6351 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 6888-6889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 7288-7290 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T93 7411-7417 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T94 7493-7494 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T95 7515-7519 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T96 7531-7532 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 7582-7584 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T98 7587-7589 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T99 7647-7651 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T100 7702-7703 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 7704-7708 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T102 7870-7872 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T103 7999-8000 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 8312-8313 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 8395-8399 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T106 8706-8707 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T107 8763-8766 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T108 8763-8766 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T109 8809-8810 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 8944-8945 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 8993-9000 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T112 9158-9159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 9281-9282 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 9323-9324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 9355-9357 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T116 9438-9440 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T117 9477-9478 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 9676-9677 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 9914-9918 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 9985-9993 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T121 10010-10011 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 10034-10038 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T123 10054-10055 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 10117-10121 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T125 10430-10431 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 10580-10581 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T127 10621-10622 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T128 10661-10662 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T129 10688-10689 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 10748-10749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 10779-10783 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T132 10797-10798 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 10813-10814 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T134 11120-11121 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 11378-11379 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T136 11451-11452 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 11506-11507 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 11610-11611 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 11681-11683 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T140 11709-11710 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 11859-11860 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 12005-12006 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 12022-12023 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 12059-12063 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T145 12115-12117 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T146 12119-12120 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 12201-12202 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 12270-12271 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 12333-12334 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 12553-12554 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 12671-12672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 12848-12849 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 13146-13152 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T154 13173-13177 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T155 13192-13193 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 13221-13225 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T157 13354-13358 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T158 13383-13384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 13419-13421 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T160 13479-13483 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T161 13490-13494 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T162 13532-13533 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T163 13609-13613 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T164 13653-13657 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T165 13800-13804 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T166 13877-13883 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T167 13891-13892 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 13928-13930 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T169 13990-13994 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T170 14017-14018 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 14072-14076 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T172 14169-14170 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T173 14480-14481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 14540-14542 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T175 14682-14683 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 14693-14696 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T177 14705-14709 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T178 14894-14895 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T179 14916-14917 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 14990-14996 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T181 15059-15060 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 15099-15100 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 15415-15416 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T184 15505-15506 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T185 15762-15768 http://purl.obolibrary.org/obo/CLO_0007225 denotes labels
T186 15901-15902 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 16178-16180 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T188 16178-16180 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T189 16221-16228 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T190 16316-16318 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T191 16316-16318 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T192 16470-16472 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T193 16484-16486 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T194 16603-16604 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 16632-16633 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 16748-16749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 16903-16905 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T198 17030-17031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 17403-17411 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T200 17604-17606 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T201 17604-17606 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T202 17776-17777 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 18297-18298 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T204 18545-18546 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T205 18914-18915 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T206 18956-18957 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T207 19051-19053 http://purl.obolibrary.org/obo/CLO_0007653 denotes ME
T208 19067-19068 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 19410-19411 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T210 19633-19634 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 19942-19943 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T212 20271-20272 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T213 21076-21077 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T214 21089-21091 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T215 21238-21239 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T216 21296-21297 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 21875-21877 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T218 21887-21889 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T219 21967-21971 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T220 21975-21977 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T221 21989-21991 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T222 22093-22095 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T223 22105-22107 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T224 22221-22222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T225 22334-22335 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T226 22430-22432 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4C
T227 22498-22499 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T228 22518-22520 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T229 22878-22879 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T230 23028-23029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T231 23299-23301 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T232 23330-23332 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T233 23361-23368 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T234 23428-23429 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T235 23514-23518 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T236 23735-23739 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T237 23802-23808 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T238 23890-23895 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T239 23982-23987 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T240 24021-24023 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T241 24075-24082 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T242 24095-24100 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T243 24356-24363 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T244 24746-24753 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T245 24863-24869 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T246 24965-24971 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T247 25027-25033 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T248 25152-25155 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T249 25317-25318 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T250 25364-25365 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T251 25453-25454 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T252 25489-25490 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 25648-25649 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 25717-25718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T255 25756-25757 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T256 25915-25916 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T257 25927-25928 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T258 26306-26307 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T259 26421-26422 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T260 26496-26497 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T261 26780-26787 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T262 27047-27049 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T263 27053-27055 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T264 27067-27069 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T265 27077-27079 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T266 27081-27083 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T267 27206-27211 http://purl.obolibrary.org/obo/CLO_0001046 denotes 1 16
T268 27222-27224 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T269 27232-27234 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T270 27246-27248 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T271 27291-27293 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T272 27476-27477 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T273 27597-27598 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T274 28268-28269 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T275 28402-28403 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T276 28777-28778 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T277 28813-28814 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T278 29069-29076 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T279 29502-29503 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T280 29868-29869 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T281 30034-30035 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T282 30135-30136 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T283 30148-30155 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T284 30185-30191 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T285 30243-30245 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T286 30268-30269 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T287 30291-30295 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T288 30322-30323 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T289 30363-30364 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T290 30734-30735 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T291 30835-30836 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T292 30852-30854 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T293 31026-31027 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T294 31102-31103 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T295 31264-31265 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T296 31304-31305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T297 31328-31329 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T298 31396-31402 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T299 31408-31410 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T300 31972-31975 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T301 32015-32017 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T302 32019-32021 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T303 32282-32284 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T304 32451-32453 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T305 32683-32684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T306 33110-33111 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T307 33128-33132 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T308 33304-33305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T309 33369-33370 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T310 33663-33665 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T311 33747-33751 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T312 33797-33798 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T313 33971-33973 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T314 33978-33979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T315 34010-34012 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T316 34072-34078 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T317 34220-34221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T318 34300-34310 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T319 34386-34387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T320 34409-34410 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T321 35070-35071 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T322 35166-35167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T323 35198-35205 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T324 35266-35273 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T325 35358-35361 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T326 35559-35562 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T327 35824-35825 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T328 35887-35892 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T329 35909-35910 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 36040-36044 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T331 36097-36098 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 36131-36132 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T333 36140-36144 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T334 36176-36177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T335 36220-36221 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T336 36275-36277 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T337 36325-36326 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T338 36879-36880 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T339 37290-37297 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T340 37503-37504 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T341 37523-37530 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T342 37843-37844 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 37930-37937 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T344 38165-38166 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 38394-38399 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T346 38467-38468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T347 38516-38517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T348 38650-38651 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T349 38679-38680 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T350 38707-38714 http://purl.obolibrary.org/obo/UBERON_0001042 denotes pharynx
T351 38707-38714 http://purl.obolibrary.org/obo/UBERON_0006562 denotes pharynx
T352 38886-38887 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T353 39030-39031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 39352-39355 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T355 39493-39500 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T356 39568-39573 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T357 39632-39639 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T358 39643-39644 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T359 39676-39683 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T360 39842-39846 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T361 39881-39886 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T362 39898-39903 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T363 39931-39932 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 39986-39990 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T365 40076-40077 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T366 40201-40207 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T367 40620-40627 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T368 40716-40720 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T369 40745-40750 http://www.ebi.ac.uk/efo/EFO_0000825 denotes mouth
T370 40889-40890 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T371 40979-40986 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T372 41740-41747 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T373 41829-41830 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T374 41867-41868 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T375 41953-41954 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T376 42282-42289 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T377 42338-42340 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T378 42447-42448 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T379 42500-42503 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T380 42556-42557 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T381 42626-42627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T382 42901-42906 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T383 42967-42974 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T384 43051-43052 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T385 43139-43140 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T386 43329-43335 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T387 43503-43506 http://purl.obolibrary.org/obo/CLO_0008190 denotes Per
T388 43612-43617 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T389 43702-43706 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T390 43761-43767 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T391 43819-43823 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T392 44020-44025 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T393 44232-44233 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T394 44261-44265 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T395 44267-44268 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T396 44297-44301 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T397 44341-44342 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T398 44475-44477 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T399 44499-44503 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T400 44744-44746 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T401 44782-44786 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T402 44806-44807 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T403 45008-45009 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T404 45402-45406 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T405 45475-45479 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T406 45483-45484 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T407 45509-45510 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T408 45795-45796 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T409 45879-45880 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T410 45906-45907 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T411 45962-45968 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T412 46316-46323 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T413 46335-46336 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T414 46403-46404 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T415 46955-46956 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T416 47057-47058 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T417 47438-47439 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T418 47530-47531 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T419 47827-47831 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T420 47984-47985 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T421 48228-48229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T422 48475-48476 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T423 48602-48603 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T424 48685-48686 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T425 48826-48827 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T426 48896-48897 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T427 48993-48996 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T428 49100-49101 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T429 49412-49413 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T430 49744-49745 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T431 50218-50219 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 50336-50338 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T433 50666-50670 http://purl.obolibrary.org/obo/PR_000002979 denotes TAPS
T434 50734-50735 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T435 50783-50789 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T436 50881-50882 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T437 50977-50978 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T438 51537-51538 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T439 51918-51921 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T440 51918-51921 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T441 52088-52089 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T442 52119-52120 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T443 52210-52212 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T444 52232-52234 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T445 52286-52288 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T446 52725-52730 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T447 52810-52812 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T448 52868-52873 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T449 52891-52892 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T450 52937-52938 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T451 52960-52961 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T452 53052-53053 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T453 53377-53378 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T454 53402-53403 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T455 53426-53430 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T456 53687-53690 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T457 53719-53720 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T458 53825-53830 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T459 53869-53870 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T460 53902-53907 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T461 54088-54089 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T462 54436-54437 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T463 55028-55030 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T464 55296-55297 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 613-621 Chemical denotes carriers http://purl.obolibrary.org/obo/CHEBI_78059
T2 1347-1355 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T3 1418-1426 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T4 1570-1586 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T5 2045-2048 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6 2081-2084 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T7 2117-2133 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T8 2283-2298 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T9 2299-2304 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T10 2320-2335 Chemical denotes fluorescent dye http://purl.obolibrary.org/obo/CHEBI_51121
T11 2332-2335 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T12 2655-2663 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T13 3202-3205 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T14 3312-3315 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T15 3316-3332 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T16 3392-3401 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T17 3503-3519 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T18 3581-3597 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T19 3606-3609 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T20 3641-3644 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T21 3735-3738 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T22 3789-3798 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T23 3867-3875 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T24 3950-3953 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T25 4055-4064 Chemical denotes indicator http://purl.obolibrary.org/obo/CHEBI_47867
T26 4072-4082 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T27 4072-4078 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T28 4495-4498 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T29 4732-4741 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T30 4878-4881 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T31 6772-6775 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T32 6956-6963 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T33 6973-6988 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T34 6995-7003 Chemical denotes aptamers http://purl.obolibrary.org/obo/CHEBI_140488
T35 7054-7064 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T36 7617-7632 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T37 7689-7698 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T38 7735-7743 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T39 8173-8182 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T40 8365-8374 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T41 8768-8775 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T42 8898-8907 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T43 9634-9644 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T44 9634-9640 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T45 9691-9694 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T46 11049-11059 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T47 11049-11055 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T48 11541-11547 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T49 11552-11555 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T50 12368-12377 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T51 12771-12780 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T52 14109-14111 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T53 16178-16180 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T54 16316-16318 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T55 17182-17189 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T56 17604-17606 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T57 18233-18236 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T58 18776-18779 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T59 20474-20476 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T60 21089-21091 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T61 22980-22988 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T62 23108-23114 Chemical denotes silica http://purl.obolibrary.org/obo/CHEBI_30563
T63 23705-23714 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T64 23861-23870 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T65 26737-26739 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T66 26875-26877 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T67 29941-29944 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T68 30883-30892 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T69 32425-32433 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T70 32482-32488 Chemical denotes silica http://purl.obolibrary.org/obo/CHEBI_30563
T71 33907-33922 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T72 34250-34253 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T73 34395-34400 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T74 34513-34521 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T75 34660-34668 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T76 34733-34741 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T77 34941-34944 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T78 35508-35520 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T79 35733-35745 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T80 35826-35838 Chemical denotes template RNA http://purl.obolibrary.org/obo/CHEBI_33699
T81 36670-36673 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T82 37621-37629 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T83 39089-39097 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T84 39220-39228 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T85 42634-42640 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T86 43289-43297 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T87 43434-43439 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T88 43569-43574 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T89 43708-43711 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T90 43825-43828 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T91 43915-43918 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T92 44282-44291 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T93 44594-44602 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T94 44604-44609 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T95 44657-44672 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T96 44877-44880 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T97 44916-44932 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T98 45325-45330 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T99 45867-45875 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T100 46127-46135 Chemical denotes aluminum http://purl.obolibrary.org/obo/CHEBI_28984
T101 46147-46149 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T102 46386-46393 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T93821 46892-46897 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T20136 47305-47313 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T63187 47329-47332 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T68111 48078-48088 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T61897 48078-48084 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T63691 49853-49856 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T55476 49922-49924 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T75557 50122-50126 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T83003 50127-50130 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T99414 50381-50385 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T12523 50386-50389 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T47167 50525-50528 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6045 50597-50603 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T74345 50612-50616 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T27218 50617-50630 Chemical denotes hydroxymethyl http://purl.obolibrary.org/obo/CHEBI_24712
T25862 50631-50642 Chemical denotes methylamino http://purl.obolibrary.org/obo/CHEBI_44209
T6351 50659-50663 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T29057 50688-50693 Chemical denotes MgCl2 http://purl.obolibrary.org/obo/CHEBI_6636
T54464 50874-50877 Chemical denotes SDS http://purl.obolibrary.org/obo/CHEBI_8984
T50580 50924-50927 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T56525 51137-51142 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T73443 51347-51354 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T70592 51411-51415 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T8179 51416-51419 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T97460 51923-51930 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T41618 51931-51935 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T95865 51936-51943 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T15569 51944-51948 Chemical denotes EDTA http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755
T86686 52887-52889 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T89454 54731-54734 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
55 77-87 Species denotes SARS-CoV-2 Tax:2697049
56 89-136 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
57 138-149 Species denotes coronavirus Tax:11118
58 218-224 Species denotes people Tax:9606
59 451-457 Species denotes people Tax:9606
60 585-595 Species denotes SARS-CoV-2 Tax:2697049
61 715-723 Species denotes patients Tax:9606
62 17-41 Disease denotes coronavirus disease 2019 MESH:C000657245
63 43-51 Disease denotes COVID-19 MESH:C000657245
64 327-335 Disease denotes COVID-19 MESH:C000657245
65 495-515 Disease denotes SARS-CoV-2 infection MESH:C000657245
66 571-579 Disease denotes infected MESH:D007239
67 662-671 Disease denotes infection MESH:D007239
71 969-976 Species denotes persons Tax:9606
72 960-968 Disease denotes infected MESH:D007239
73 1004-1013 Disease denotes infection MESH:D007239
79 1371-1376 Species denotes human Tax:9606
80 1621-1631 Species denotes SARS-CoV-2 Tax:2697049
81 1407-1417 Species denotes SARS-CoV-2 Tax:2697049
82 1570-1586 Chemical denotes oligonucleotides MESH:D009841
83 1263-1283 Disease denotes SARS-CoV-2 infection MESH:C000657245
87 1678-1688 Species denotes SARS-CoV-2 Tax:2697049
88 2117-2133 Chemical denotes oligonucleotides MESH:D009841
89 2283-2298 Chemical denotes oligonucleotide MESH:D009841
92 2861-2871 Species denotes SARS-CoV-2 Tax:2697049
93 2624-2632 Disease denotes COVID-19 MESH:C000657245
98 3316-3332 Chemical denotes oligonucleotides MESH:D009841
99 3503-3519 Chemical denotes oligonucleotides MESH:D009841
100 3581-3597 Chemical denotes oligonucleotides MESH:D009841
101 3896-3925 Chemical denotes deoxynucleotide triphosphates
108 4175-4177 Gene denotes pH Gene:5053
109 4052-4054 Gene denotes pH Gene:5053
110 4412-4427 Species denotes influenza virus Tax:11309
111 4540-4550 Species denotes SARS-CoV-2 Tax:2697049
112 4777-4787 Species denotes SARS-CoV-2 Tax:2697049
113 4072-4082 Chemical denotes phenol red MESH:D010637
118 5744-5754 Species denotes SARS-CoV-2 Tax:2697049
119 5984-5994 Species denotes SARS-CoV-2 Tax:2697049
120 5607-5615 Disease denotes COVID-19 MESH:C000657245
121 5867-5875 Disease denotes COVID-19 MESH:C000657245
123 6651-6661 Species denotes SARS-CoV-2 Tax:2697049
135 7547-7574 Gene denotes open reading frame (ORF) 1a Gene:43740578
136 6816-6819 Gene denotes mix Gene:83881
137 6767-6770 Gene denotes Mix Gene:83881
138 7645-7646 Gene denotes N Gene:43740575
139 7513-7514 Gene denotes N Gene:43740575
140 7491-7492 Gene denotes N Gene:43740575
141 6685-6695 Species denotes SARS-CoV-2 Tax:2697049
142 7256-7266 Species denotes SARS-CoV-2 Tax:2697049
143 7468-7478 Species denotes SARS-CoV-2 Tax:2697049
144 6973-6988 Chemical denotes oligonucleotide MESH:D009841
145 7617-7632 Chemical denotes oligonucleotide MESH:D009841
151 8393-8394 Gene denotes N Gene:43740575
152 8382-8392 Species denotes SARS-CoV-2 Tax:2697049
153 8883-8893 Species denotes SARS-CoV-2 Tax:2697049
154 8536-8539 Chemical denotes ice MESH:D007053
155 8768-8775 Chemical denotes agarose MESH:D012685
158 9678-9680 Gene denotes pH Gene:5053
159 9634-9644 Chemical denotes phenol red MESH:D010637
164 10777-10778 Gene denotes N Gene:43740575
165 10795-10796 Gene denotes N Gene:43740575
166 10766-10776 Species denotes SARS-CoV-2 Tax:2697049
167 11049-11059 Chemical denotes phenol red MESH:D010637
170 11984-11991 Species denotes patient Tax:9606
171 11541-11547 Chemical denotes phenol MESH:D019800
173 12846-12847 Gene denotes N Gene:43740575
179 13821-13825 Gene denotes RdRp Gene:43740578
180 13607-13608 Gene denotes N Gene:43740575
181 13352-13353 Gene denotes N Gene:43740575
182 13219-13220 Gene denotes N Gene:43740575
183 13680-13690 Species denotes SARS-CoV-2 Tax:2697049
187 13921-13926 Gene denotes ORF1a Gene:43740578
188 13988-13989 Gene denotes N Gene:43740575
189 14167-14168 Gene denotes N Gene:43740575
191 14335-14345 Species denotes SARS-CoV-2 Tax:2697049
193 14723-14737 Gene denotes 3A and Table 1
195 14853-14863 Species denotes SARS-CoV-2 Tax:2697049
197 16122-16128 Disease denotes Wilson MESH:D006527
203 17286-17300 Gene denotes 3A and Table 1
204 16692-16702 Species denotes SARS-CoV-2 Tax:2697049
205 16987-16997 Species denotes SARS-CoV-2 Tax:2697049
206 17419-17425 Disease denotes Wilson MESH:D006527
207 17536-17542 Disease denotes Wilson MESH:D006527
209 19688-19698 Species denotes SARS-CoV-2 Tax:2697049
211 23108-23118 Chemical denotes silica gel MESH:D058428
217 23733-23734 Gene denotes N Gene:43740575
218 23722-23732 Species denotes SARS-CoV-2 Tax:2697049
219 24297-24307 Species denotes SARS-CoV-2 Tax:2697049
220 23763-23771 Disease denotes COVID-19 MESH:C000657245
221 24333-24341 Disease denotes infected MESH:D007239
223 27331-27333 Gene denotes pH Gene:5053
225 27656-27658 Gene denotes pH Gene:5053
228 29247-29249 Gene denotes pH Gene:5053
229 29386-29398 Chemical denotes Amies medium
232 30032-30033 Gene denotes N Gene:43740575
233 29809-29829 Disease denotes SARS-CoV-2 infection MESH:C000657245
238 30339-30344 Gene denotes ORF1a Gene:43740578
239 30289-30290 Gene denotes N Gene:43740575
240 30266-30267 Gene denotes N Gene:43740575
241 30489-30499 Species denotes SARS-CoV-2 Tax:2697049
245 31262-31263 Gene denotes N Gene:43740575
246 31045-31055 Species denotes SARS-CoV-2 Tax:2697049
247 31306-31326 Disease denotes SARS-CoV-2 infection MESH:C000657245
249 32482-32488 Chemical denotes silica MESH:D012822
252 33725-33735 Species denotes SARS-CoV-2 Tax:2697049
253 33907-33922 Chemical denotes oligonucleotide MESH:D009841
255 34395-34400 Chemical denotes water MESH:D014867
257 35255-35265 Species denotes SARS-CoV-2 Tax:2697049
261 35689-35691 Gene denotes pH Gene:5053
262 35614-35616 Gene denotes pH Gene:5053
263 36107-36123 Disease denotes reaction failure MESH:D006333
269 38383-38393 Species denotes SARS-CoV-2 Tax:2697049
270 38167-38187 Disease denotes SARS-CoV-2 infection MESH:C000657245
271 38469-38489 Disease denotes SARS-CoV-2 infection MESH:C000657245
272 38584-38592 Disease denotes COVID-19 MESH:C000657245
273 38773-38781 Disease denotes infected MESH:D007239
278 40108-40118 Species denotes SARS-CoV-2 Tax:2697049
279 40566-40573 Species denotes patient Tax:9606
280 40212-40220 Disease denotes COVID-19 MESH:C000657245
281 40326-40346 Disease denotes SARS-CoV-2 infection MESH:C000657245
285 41001-41011 Species denotes SARS-CoV-2 Tax:2697049
286 41277-41287 Species denotes SARS-CoV-2 Tax:2697049
287 41352-41362 Species denotes SARS-CoV-2 Tax:2697049
289 42134-42146 Chemical denotes Amies medium
296 44073-44076 Gene denotes mix Gene:83881
297 43534-43537 Gene denotes mix Gene:83881
298 43236-43246 Species denotes SARS-CoV-2 Tax:2697049
299 43696-43699 Species denotes CoV Tax:11118
300 43813-43816 Species denotes CoV Tax:11118
301 43569-43574 Chemical denotes water MESH:D014867
307 44487-44492 Gene denotes ORF1a Gene:43740578
308 44497-44498 Gene denotes N Gene:43740575
309 44691-44694 Gene denotes mix Gene:83881
310 44604-44609 Chemical denotes water MESH:D014867
311 44657-44672 Chemical denotes oligonucleotide MESH:D009841
314 44780-44781 Gene denotes N Gene:43740575
315 44838-44839 Gene denotes N Gene:43740575
323 45680-45683 Gene denotes mix Gene:83881
324 45595-45598 Gene denotes mix Gene:83881
325 45427-45430 Gene denotes mix Gene:83881
326 45289-45292 Gene denotes mix Gene:83881
327 45325-45330 Chemical denotes water MESH:D014867
328 46127-46135 Chemical denotes aluminum MESH:D000535
329 46386-46393 Chemical denotes agarose MESH:D012685
336 46758-46761 Gene denotes Mix Gene:83881
337 47021-47024 Gene denotes mix Gene:83881
338 46841-46844 Gene denotes mix Gene:83881
339 46892-46897 Chemical denotes water MESH:D014867
340 47329-47332 Chemical denotes CO2 MESH:D002245
341 47726-47731 Chemical denotes metal MESH:D008670
343 47923-47930 Gene denotes RT-LAMP
345 48078-48088 Chemical denotes phenol red MESH:D010637
352 49145-49148 Gene denotes mix Gene:83881
353 48586-48589 Gene denotes mix Gene:83881
354 48424-48431 Species denotes patient Tax:9606
355 49061-49068 Species denotes patient Tax:9606
356 48764-48769 Chemical denotes metal MESH:D008670
357 49610-49615 Chemical denotes metal MESH:D008670
372 50132-50134 Gene denotes pH Gene:5053
373 50234-50245 Species denotes Transposons Tax:2387
374 50122-50126 Chemical denotes tris
375 50127-50130 Chemical denotes HCl MESH:D006851
376 50874-50877 Chemical denotes SDS MESH:D012967
377 51137-51142 Chemical denotes water MESH:D014867
378 51347-51354 Chemical denotes ethanol MESH:D000431
379 51411-51419 Chemical denotes tris-HCl
380 51923-51930 Chemical denotes agarose MESH:D012685
381 51931-51943 Chemical denotes tris-acetate
382 51944-51948 Chemical denotes EDTA MESH:D004492
383 50666-50670 Disease denotes TAPS
384 50275-50279 Mutation denotes E54K p.E54K
385 50281-50286 Mutation denotes L372P p.L372P
388 52887-52898 Gene denotes S4, B and C Gene:6192
389 52612-52622 Species denotes SARS-CoV-2 Tax:2697049
392 53424-53425 Gene denotes N Gene:43740575
393 53413-53423 Species denotes SARS-CoV-2 Tax:2697049
395 54713-54716 Gene denotes S5B Gene:5711
397 55573-55579 Disease denotes Wilson MESH:D006527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T25 1944-1946 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T26 1984-1997 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T27 1984-1997 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T28 1999-2001 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T29 2772-2781 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T30 2831-2833 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T31 3057-3059 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T32 3068-3089 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T33 3076-3089 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T34 3130-3132 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T35 3146-3148 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T36 3182-3195 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T37 3182-3195 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T38 3229-3248 http://purl.obolibrary.org/obo/GO_0000732 denotes strand displacement
T39 3551-3564 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T40 3551-3564 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T41 3968-3970 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T42 4323-4325 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T43 4495-4512 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T44 4878-4895 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T45 5172-5174 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T46 5716-5718 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T47 6010-6012 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T48 6058-6060 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T49 6317-6319 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T50 6503-6505 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T51 6605-6607 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T52 6705-6707 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T53 6749-6751 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T54 6864-6877 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T55 6864-6877 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T56 7229-7231 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T57 8025-8027 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T58 8130-8132 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T59 8271-8273 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T60 8418-8420 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T61 8713-8715 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T62 8822-8824 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T63 9044-9046 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T64 9087-9089 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T65 9170-9172 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T66 9229-9231 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T67 9906-9908 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T68 9977-9979 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T69 10276-10278 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T70 10302-10304 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T71 10410-10412 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T72 10451-10453 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T73 10723-10725 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T74 11267-11269 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T75 11408-11410 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T76 11466-11468 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T77 12051-12053 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T78 12239-12241 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T79 12284-12286 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T80 12297-12299 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T81 12513-12515 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T82 12625-12627 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T83 12656-12658 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T84 12789-12791 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T85 12874-12876 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T86 13111-13113 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T87 13201-13203 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T88 13300-13302 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T89 13698-13700 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T90 13854-13856 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T91 14077-14079 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T92 14190-14192 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T93 14236-14238 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T94 14317-14319 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T95 14412-14414 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T96 14566-14568 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T97 14655-14663 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T98 14760-14762 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T99 14878-14880 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T100 14932-14934 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T101 14958-14960 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T102 15185-15187 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T103 15382-15384 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T104 15398-15400 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T105 15468-15470 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T106 15567-15569 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T107 15632-15634 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T108 15668-15670 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T109 15926-15928 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T110 16201-16203 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T111 16213-16215 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T112 16390-16392 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T113 16418-16420 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T114 16718-16720 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T115 16781-16783 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T116 16956-16958 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T117 17213-17215 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T118 17266-17268 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T119 17395-17397 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T120 17517-17519 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T121 17636-17638 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T122 17706-17708 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T123 17884-17886 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T124 17979-17981 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T125 18047-18049 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T126 18359-18361 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T127 18638-18640 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T128 18868-18870 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T129 19108-19110 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T130 19533-19535 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T131 19580-19582 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T132 19911-19913 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T133 20114-20116 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T134 20196-20198 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T135 20380-20382 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T136 21219-21221 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T137 21307-21309 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T138 21350-21352 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T139 21415-21417 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T140 21453-21455 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T141 21538-21540 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T142 21550-21552 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T143 21638-21640 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T144 21769-21771 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T145 21823-21825 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T146 21927-21929 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T147 22045-22047 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T148 22199-22201 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T149 22468-22470 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T150 22773-22775 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T151 22862-22864 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T152 22888-22890 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T153 23290-23292 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T154 23310-23312 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T155 23489-23491 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T156 23550-23552 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T157 24154-24156 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T158 24398-24400 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T159 24544-24546 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T160 24614-24616 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T161 24806-24808 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T162 24914-24916 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T163 24994-24996 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T164 25193-25195 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T165 25240-25242 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T166 25294-25296 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T167 25424-25426 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T168 25553-25555 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T169 25863-25865 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T170 26001-26003 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T171 26151-26153 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T172 26206-26208 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T173 26380-26382 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T174 26657-26659 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T175 26706-26708 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T176 26760-26762 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T177 26772-26774 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T178 26961-26963 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T179 26972-26974 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T180 27001-27003 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T181 27140-27142 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T182 27151-27153 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T183 27180-27182 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T184 27349-27351 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T185 27411-27413 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T186 27434-27436 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T187 27817-27819 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T188 27876-27878 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T189 28376-28378 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T190 28483-28485 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T191 28649-28651 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T192 28929-28931 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T193 29305-29307 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T194 29459-29461 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T195 29697-29699 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T196 29774-29776 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T197 29941-29958 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T198 30008-30010 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T199 30082-30084 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T200 30196-30198 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T201 30388-30390 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T202 30521-30523 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T203 30645-30647 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T204 30745-30747 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T205 30961-30963 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T206 31207-31209 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T207 31547-31549 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T208 31762-31764 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T209 31929-31931 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T210 32080-32082 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T211 32138-32140 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T212 32387-32397 http://purl.obolibrary.org/obo/GO_0004175 denotes proteinase
T213 32569-32571 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T214 32629-32631 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T215 32885-32887 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T216 33120-33122 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T217 33284-33286 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T218 33348-33350 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T219 34169-34171 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T220 34187-34189 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T221 34203-34205 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T222 34250-34267 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T223 34345-34347 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T224 34441-34443 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T225 34530-34532 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T226 34581-34583 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T227 34652-34654 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T228 34725-34727 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T229 34801-34803 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T230 34895-34897 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T231 35018-35020 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T232 35107-35109 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T233 35223-35225 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T234 35344-35346 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T235 35454-35456 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T236 35541-35543 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T237 35637-35639 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T238 35763-35776 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T239 35879-35881 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T240 36205-36207 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T241 36414-36416 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T242 36961-36963 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T243 37368-37370 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T244 37453-37455 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T245 37607-37609 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T246 38088-38090 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T247 38257-38259 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T248 38288-38290 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T249 38842-38844 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T250 38960-38962 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T251 39047-39049 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T252 39130-39132 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T253 39289-39291 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T254 39338-39340 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T255 39438-39440 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T256 39554-39556 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T257 39592-39594 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T258 39778-39780 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T259 39913-39915 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T260 40350-40352 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T261 40486-40497 http://purl.obolibrary.org/obo/GO_0065007 denotes regulations
T262 40904-40906 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T263 40971-40973 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T264 41222-41224 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T265 41553-41555 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T266 41685-41687 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T267 41732-41734 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T268 41929-41931 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T269 42366-42377 http://purl.obolibrary.org/obo/GO_0006810 denotes transported
T270 42628-42633 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T271 42661-42663 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T272 43198-43200 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T273 43972-43985 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T274 43972-43985 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T275 44204-44206 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T276 44310-44312 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T277 44353-44355 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T278 44400-44402 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T279 44543-44552 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T280 44708-44710 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T281 45394-45396 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T282 45412-45414 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T283 45587-45589 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T284 45993-45995 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T285 46230-46232 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T286 46425-46427 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T287 46564-46566 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T288 46740-46742 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T289 47345-47358 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T290 47923-47925 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T291 48122-48135 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T292 48367-48369 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T293 48408-48410 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T294 49336-49338 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T295 49710-49712 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T296 49853-49870 http://purl.obolibrary.org/obo/GO_0006309 denotes DNA fragmentation
T297 50500-50502 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T298 51474-51476 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T299 53523-53525 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T300 54161-54163 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T301 54749-54751 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T302 54803-54805 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T303 55161-55163 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T304 55209-55211 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T305 55265-55267 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T306 55370-55372 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T307 55429-55431 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 6404-6407 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T2 18111-18114 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T3 19084-19087 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T4 41955-41958 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T5 49790-49793 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T6 50271-50274 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T7 51495-51498 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T21 0-12 Sentence denotes INTRODUCTION
T22 13-187 Sentence denotes The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus (1), is a major global health threat.
T23 188-399 Sentence denotes A still unknown proportion of people, especially the elderly and those with preexisting conditions, are at high risk of a severe course of COVID-19 (2), leading to a high burden on health care systems worldwide.
T24 400-642 Sentence denotes Further, because of limited testing capacity, only people with symptoms are usually tested for SARS-CoV-2 infection, although studies have confirmed that many individuals infected with SARS-CoV-2 are asymptomatic carriers of the virus (3, 4).
T25 643-767 Sentence denotes This suggests that infection control strategies focusing on symptomatic patients are not sufficient to prevent virus spread.
T26 768-915 Sentence denotes Therefore, large-scale diagnostic methods are needed to determine the spread of the virus in populations quickly, comprehensively, and sensitively.
T27 916-1014 Sentence denotes This would allow for the rapid isolation of infected persons during an existing wave of infection.
T28 1015-1252 Sentence denotes In addition, continuous and repeated testing of large groups within a population may be required as a long-term strategy to contain new outbreaks while keeping societies and economies functional until effective vaccines become available.
T29 1253-1385 Sentence denotes An active SARS-CoV-2 infection can be diagnosed by detecting either the viral genome or viral antigens in appropriate human samples.
T30 1386-1587 Sentence denotes Assays for detecting SARS-CoV-2 antigens are limited by the sensitivity, specificity, and production speed of diagnostic antibodies, whereas detecting viral RNA only requires specific oligonucleotides.
T31 1588-1673 Sentence denotes Therefore, an assay that detects SARS-CoV-2 RNA facilitates testing of large cohorts.
T32 1674-1952 Sentence denotes The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR.
T33 1953-2169 Sentence denotes The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR).
T34 2170-2336 Sentence denotes As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye.
T35 2337-2588 Sentence denotes This procedure includes several steps that require sample handling; therefore, the detection process in a clinical diagnostic laboratory takes about 3 to 24 hours or more, depending on the number of samples and process optimization of the test center.
T36 2589-2782 Sentence denotes In addition, in the context of the COVID-19 pandemic, many of the reagents required are only slowly being replenished due to insufficient production capacity or lack of international transport.
T37 2783-2907 Sentence denotes Therefore, increasing daily test capacities for RT-qPCR–based diagnostics for SARS-CoV-2 RNA detection is currently limited.
T38 2908-3038 Sentence denotes To accelerate and optimize such diagnostics, new scalable methods for RNA isolation and the detection of viral genomes are needed.
T39 3039-3145 Sentence denotes An alternative to RT-qPCR is reverse transcription loop-mediated isothermal amplification (RT-LAMP) (5–7).
T40 3146-3359 Sentence denotes RT-LAMP reactions include a reverse transcriptase and a DNA polymerase with strong strand displacement activity and tolerance for elevated temperatures and up to six DNA oligonucleotides of a certain architecture.
T41 3360-3498 Sentence denotes Samples with potential template molecules are added to the reaction and incubated for 20 to 60 min at a constant temperature (e.g., 65°C).
T42 3499-3678 Sentence denotes The oligonucleotides act as primers for the reverse transcriptase, and additional oligonucleotides for the DNA polymerase are designed so the DNA products loop back at their ends.
T43 3679-3750 Sentence denotes These, in turn, serve as self-priming templates for the DNA polymerase.
T44 3751-3939 Sentence denotes In the presence of a few RNA template molecules, a chain reaction is set in motion, which then runs until the added reagents (in particular, the deoxynucleotide triphosphates) are used up.
T45 3940-4023 Sentence denotes To detect DNA production in RT-LAMP assays, various approaches have been described.
T46 4024-4138 Sentence denotes One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment.
T47 4139-4310 Sentence denotes 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).
T48 4311-4432 Sentence denotes Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9).
T49 4433-4555 Sentence denotes Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA.
T50 4556-4755 Sentence denotes 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.
T51 4756-5008 Sentence denotes 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.
T52 5009-5149 Sentence denotes Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples.
T53 5150-5430 Sentence denotes 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.
T54 5431-5576 Sentence denotes For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used.
T55 5577-6029 Sentence denotes 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).
T56 6030-6168 Sentence denotes We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step.
T57 6169-6331 Sentence denotes We tested >700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay.
T58 6332-6568 Sentence denotes 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.
T59 6570-6577 Sentence denotes RESULTS
T60 6579-6674 Sentence denotes Establishing colorimetric RT-LAMP assay sensitivity using an artificial SARS-CoV-2 RNA template
T61 6675-6810 Sentence denotes To detect SARS-CoV-2 RNA with RT-LAMP, we used the WarmStart Colorimetric RT-LAMP 2X Master Mix (DNA and RNA) from New England Biolabs.
T62 6811-6929 Sentence denotes This mix contains two enzymes, an engineered reverse transcriptase (RTx) and a strand-displacing polymerase (Bst 2.0).
T63 6930-7181 Sentence denotes In addition, the reaction mixture contains oligonucleotide-based aptamers that function as reversible temperature-dependent inhibitors, ensuring that the reaction only runs at an elevated temperature (WarmStart) to avoid nonspecific priming reactions.
T64 7182-7394 Sentence denotes Several primer sets were recently proposed for RT-LAMP–based detection of SARS-CoV-2 RNA by Zhang et al. (11) and by Yu et al. (10), and these primer sets were subsequently validated with in vitro–translated RNA.
T65 7395-7591 Sentence denotes We prepared and tested two primer sets for different RNA sections of the SARS-CoV-2 genome, the N-A set targeting the N gene and the 1a-A set targeting open reading frame (ORF) 1a (table S1) (11).
T66 7592-7792 Sentence denotes Figure 1A shows that the oligonucleotide set for the N gene was capable of detecting 100 IVT RNA molecules in a test reaction with 1 μl of RNA solution, as evidenced by the red-to-yellow color change.
T67 7793-7845 Sentence denotes The reaction was conducted for up to 1 hour at 65°C.
T68 7846-7937 Sentence denotes For time points > 30 to 35 min, the negative control frequently became yellowish (Fig. 1A).
T69 7938-8038 Sentence denotes This was caused by spurious amplification products, which is a well-known problem with RT-LAMP (14).
T70 8039-8243 Sentence denotes Analysis by gel electrophoresis revealed clearly distinct banding patterns for the correct RT-LAMP reaction products (lanes with ≥100 molecules IVT RNA input) and the spurious reaction products (Fig. 1B).
T71 8244-8310 Sentence denotes Fig. 1 Sensitivity of the RT-LAMP assay determined using IVT RNA.
T72 8311-8457 Sentence denotes (A) Defined numbers of in vitro transcribed (IVT) RNA molecules of the SARS-CoV-2 N gene were added to the RT-LAMP reaction and incubated at 65°C.
T73 8458-8561 Sentence denotes At indicated times, samples were removed from the heating block and cooled on ice to stop the reaction.
T74 8562-8780 Sentence denotes Photographs were taken using the color scanner function of an office copy machine and show the red to yellow color change in positive samples. (B) The RT-LAMP reaction product (2.5 μl) was analyzed on a 2% agarose gel.
T75 8781-8991 Sentence denotes The typical band pattern of a successful RT-LAMP reaction was visible in the samples with 100 or more SARS-CoV-2 RNA molecules, i.e., in those samples that showed a color change from red to yellow after 30 min.
T76 8993-9057 Sentence denotes Testing clinical RNA samples with the colorimetric RT-LAMP assay
T77 9058-9185 Sentence denotes To evaluate the colorimetric RT-LAMP assay, we needed to compare its sensitivity and specificity to a validated RT-qPCR method.
T78 9186-9310 Sentence denotes We first used 95 RNA samples and performed RT-LAMP reactions using 1 μl of the isolated RNA in a reaction volume of 12.5 μl.
T79 9311-9442 Sentence denotes We detected a red-to-yellow color change in 36 of the samples following an incubation of the reaction for 30 min at 65°C (Fig. 2A).
T80 9443-9719 Sentence denotes To quantify the reaction, we used a plate scanner and measured the difference in absorbance (ΔOD) of the samples at 434 and 560 nm (corresponding to the absorbance maxima of the two forms of phenol red that were used in the assay as a pH-sensitive dye) at several time points.
T81 9720-9971 Sentence denotes To visualize the data, we plotted the ΔOD values against incubation time and colored the time traces of individual samples according to the cycle threshold (CT) values obtained from the RT-qPCR test run in the clinical diagnostic laboratory (Fig. 2B).
T82 9972-10232 Sentence denotes This RT-qPCR test was performed using a commercial diagnostic test kit containing a modified version of the E-Sarbeco primer set for the viral E gene suggested by Corman et al. (15) and 10 μl of RNA isolated with an automated platform (QiaSymphony or QiaCube).
T83 10233-10333 Sentence denotes Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.
T84 10334-10446 Sentence denotes RNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate.
T85 10447-10676 Sentence denotes The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone.
T86 10677-10919 Sentence denotes Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements.
T87 10920-11087 Sentence denotes The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm.
T88 11088-11146 Sentence denotes Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4.
T89 11147-11179 Sentence denotes Each line represents one sample.
T90 11180-11416 Sentence denotes For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR.
T91 11417-11447 Sentence denotes Each dot is one sample (well).
T92 11448-11596 Sentence denotes In a colorimetric RT-LAMP reaction, positive samples with a CT < 30 changed the color of the phenol-red dye within the first 30 min of the reaction.
T93 11597-11774 Sentence denotes Samples with a CT > 30 either did not change their color or did so at time points > 35 min, simultaneously with a color change observed in some of the negative samples (Fig. 1).
T94 11775-11893 Sentence denotes On the basis of this observation, we used the ΔOD value at 30 min to decide whether a sample was positive or negative.
T95 11894-12185 Sentence denotes Plotting the ΔOD measurements versus CT values at the 30-min time point revealed that all patient samples with a CT < 30 showed a robust color change in the RT-LAMP test, whereas for samples with CT values between 30 and 35, a positive result was observed for only 1 of 10 samples (Fig. 2C).
T96 12186-12292 Sentence denotes This suggested a detection limit of the colorimetric RT-LAMP assay corresponding to a CT ≈ 30 for RT-qPCR.
T97 12293-12488 Sentence denotes The RT-qPCR kit used was calibrated and a CT ≈ 30 corresponded to 1000 RNA molecules present in the reaction according to the certificate provided by the manufacturer (see Materials and Methods).
T98 12489-12572 Sentence denotes The performance of each RT-qPCR run was validated using this as a positive control.
T99 12573-12813 Sentence denotes Considering that 10 μl of isolated RNA was used for RT-qPCR, but only 1 μl for the RT-LAMP assay, a cutoff of CT ≈ 30 agreed well with the observed experimental sensitivity of approximately 100 RNA molecules for the RT-LAMP assay (Fig. 1A).
T100 12814-12990 Sentence denotes Therefore, it appeared that the N-A primer set used for the RT-LAMP assay performed equally well with either IVT RNA or RNA samples isolated from the pharyngeal swab specimens.
T101 12991-13285 Sentence denotes In March 2020, at the beginning of the pandemic, the diagnostic laboratory that analyzed the pharyngeal swab samples by RT-qPCR validated all samples that tested positive with the E gene primer set in a second RT-qPCR using the N gene primer set, also of the Sarbeco sets of Corman et al. (15).
T102 13286-13433 Sentence denotes When plotting RT-LAMP assay results against the CT values for the N gene primer set, we observed a sensitivity cutoff of around CT ≈ 35 (fig. S2A).
T103 13434-13582 Sentence denotes Direct comparison of the CT values for the E gene and N gene primer sets for all samples revealed a difference of ~5.6 CT units (cycles) (fig. S2B).
T104 13583-13706 Sentence denotes This suggested that the N gene primers were less sensitive than the E gene primers for detecting SARS-CoV-2 RNA by RT-qPCR.
T105 13707-13845 Sentence denotes Similar differences have been observed previously for other primer sets, e.g., between the E gene primers and the RdRp-SARSr primers (16).
T106 13846-14113 Sentence denotes For the RT-LAMP assay, we also tested the 1a-A primer set directed against ORF1a (11) and found this primer set to be less sensitive than the N gene LAMP primer set, with a sensitivity cutoff of CT ≈ 25 when plotted against E gene RT-qPCR–derived CT values (fig. S3).
T107 14114-14284 Sentence denotes On the basis of these results, we decided to use the N-A primer set for the RT-LAMP assay and to compare our results with RT-qPCR performed with the E-Sarbeco primer set.
T108 14286-14359 Sentence denotes Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection
T109 14360-14468 Sentence denotes To determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples.
T110 14469-14544 Sentence denotes We assayed a total of 768 RNA samples obtained on different days (fig. S1).
T111 14545-14831 Sentence denotes Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.
T112 14832-14892 Sentence denotes Fig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.
T113 14893-15018 Sentence denotes (A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates.
T114 15019-15133 Sentence denotes The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated.
T115 15134-15249 Sentence denotes The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation.
T116 15250-15305 Sentence denotes The 96-well plate shown in Fig. 2 is not included here.
T117 15306-15531 Sentence denotes Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown.
T118 15532-15646 Sentence denotes The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay.
T119 15647-15940 Sentence denotes For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay.
T120 15941-16182 Sentence denotes The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).
T121 16183-16297 Sentence denotes Table 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).
T122 16298-16389 Sentence denotes Fig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.
T123 16390-16397 Sentence denotes RT-LAMP
T124 16398-16417 Sentence denotes CT Pos Neg Sum
T125 16418-16449 Sentence denotes RT-qPCR Pos 0–25 51 0 51
T126 16450-16466 Sentence denotes 25–30 28 2 30
T127 16467-16483 Sentence denotes 30–35 4 16 20
T128 16484-16500 Sentence denotes 35–40 0 16 16
T129 16501-16523 Sentence denotes Neg Neg 2 649 651
T130 16524-16717 Sentence denotes Sum 85 683 768 The consistency of the results during the analysis confirmed a threshold of ΔOD > +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A).
T131 16718-16917 Sentence denotes RT-qPCR–positive samples with a CT < 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B).
T132 16918-17040 Sentence denotes This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT < 30.
T133 17041-17199 Sentence denotes We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling.
T134 17200-17363 Sentence denotes We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3.
T135 17364-17452 Sentence denotes The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval:
T136 17453-17569 Sentence denotes 98.9 to 99.9%), and the sensitivity for samples with CT < 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval:
T137 17570-17608 Sentence denotes 91.4 to 99.3%) (Fig. 3B and table S2).
T138 17610-17661 Sentence denotes Multiplexed sequencing of RT-LAMP reaction products
T139 17662-17811 Sentence denotes Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C.
T140 17812-17945 Sentence denotes Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences.
T141 17946-18082 Sentence denotes To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing).
T142 18083-18166 Sentence denotes LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding.
T143 18167-18288 Sentence denotes Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing.
T144 18289-18407 Sentence denotes We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate.
T145 18408-18544 Sentence denotes After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters.
T146 18545-18656 Sentence denotes A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments.
T147 18657-18833 Sentence denotes Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A).
T148 18834-18912 Sentence denotes Fig. 4 Multiplexed sequencing of RT-LAMP reaction products (LAMP-sequencing).
T149 18913-18955 Sentence denotes (A) Workflow for LAMP-sequencing is shown.
T150 18956-19134 Sentence denotes A plate of 96 barcoded (BC) adapters with unique molecular identifiers (UMIs) and mosaic ends (ME) was used as a seed plate for Tn5 tagmentation of all RT-LAMP reaction products.
T151 19135-19251 Sentence denotes After tagmentation, each plate was pooled individually, followed by removal of excess adapters using size selection.
T152 19252-19597 Sentence denotes Each pool of tagmentation products was then amplified using primers with plate-specific barcodes, and the PCR products were analyzed by Illumina sequencing. (B) Comparison of the outcome of the three assays: LAMP-sequencing (purple, negative; green, positive; gray, too few UMIs), RT-LAMP (after 30-min incubation, y axis), and RT-qPCR (x axis).
T153 19598-19629 Sentence denotes Each dot represents one sample.
T154 19630-19789 Sentence denotes If a substantial number of the sequencing reads contained SARS-CoV-2 RNA, the sample was called positive (green), if not, then it was called negative (purple).
T155 19790-20092 Sentence denotes For some samples (gray), no LAMP-sequencing call could be made due to too few UMIs. (See also Table 2). (C) Although the RT-LAMP assay was scored after a 30-min incubation at 65°C (left), LAMP-sequencing was performed only after the samples had been incubated for another 10 min (15 min for one plate).
T156 20093-20274 Sentence denotes This panel shows the RT-LAMP assay outcome (y axis) scored after the full incubation time, whereas the RT-qPCR CT values (x axis) and LAMP-sequencing results are the same as in (B).
T157 20275-20478 Sentence denotes Of the LAMP-sequencing reads obtained, 98% mapped either to the part of the viral genome targeted by the RT-LAMP primers (80.6%) or contained short k-mers derived from primer sequences (17.4%) (fig. S4).
T158 20479-20548 Sentence denotes This indicated that LAMP-sequencing amplified the targeted sequences.
T159 20549-20715 Sentence denotes Reads containing only primer sequences were likely to be the result of spurious amplification products as these were also formed in the absence of input RNA (Fig. 1).
T160 20716-21014 Sentence denotes For quantification of individual LAMP reactions, we classified reads according to whether or not they contained viral sequences, which were not directly covered by the primers (orange segments in fig. S4A), and counted the reads for each sample (as specified by its barcode combination) (fig. S4B).
T161 21015-21093 Sentence denotes For 754 of the 768 samples, we obtained enough reads to make a call (fig. S5).
T162 21094-21270 Sentence denotes For the 754 samples that underwent successful LAMP-sequencing, the results confirmed all samples that scored positive on the RT-LAMP assay with a CT < 30 (Fig. 4B and Table 2).
T163 21271-21468 Sentence denotes For the two samples with a negative RT-qPCR result that scored positive on the RT-LAMP assay (Fig. 3), the LAMP-sequencing call agreed with the RT-qPCR result and thus corrected the RT-LAMP result.
T164 21469-21513 Sentence denotes Table 2 Summary of LAMP-sequencing results.
T165 21514-21768 Sentence denotes The cross tabulation of RT-qPCR and RT-LAMP assay results shown in Table 1 have been split into samples where sequencing of RT-LAMP reaction products (LAMP-sequencing) was positive (Pos), negative (Neg), or inconclusive (too few reads) (see also Fig. 4).
T166 21769-21776 Sentence denotes RT-LAMP
T167 21777-21796 Sentence denotes CT Pos Neg Sum
T168 21797-21854 Sentence denotes LAMP- sequencing Pos RT-qPCR Pos 0–25 49 0 49
T169 21855-21871 Sentence denotes 25–30 28 0 28
T170 21872-21886 Sentence denotes 30–35 4 0 4
T171 21887-21901 Sentence denotes 35–40 0 0 0
T172 21902-21920 Sentence denotes Neg Neg 0 0 0
T173 21921-21956 Sentence denotes Neg RT-qPCR Pos 0–25 0 0 0
T174 21957-21971 Sentence denotes 25–30 0 2 2
T175 21972-21988 Sentence denotes 30–35 0 16 16
T176 21989-22005 Sentence denotes 35–40 0 16 16
T177 22006-22028 Sentence denotes Neg Neg 2 637 639
T178 22029-22074 Sentence denotes Too few reads RT-qPCR Pos 0–25 2 0 2
T179 22075-22089 Sentence denotes 25–30 0 0 0
T180 22090-22104 Sentence denotes 30–35 0 0 0
T181 22105-22119 Sentence denotes 35–40 0 0 0
T182 22120-22140 Sentence denotes Neg Neg 0 12 12
T183 22141-22262 Sentence denotes Sum 85 683 768 LAMP-sequencing was performed using the RT-LAMP samples after a prolonged incubation of 40 min at 65°C.
T184 22263-22375 Sentence denotes At this time point, many of the negative samples and also samples with a CT between 30 and 40 had turned yellow.
T185 22376-22434 Sentence denotes LAMP-sequencing eliminated all of these samples (Fig. 4C).
T186 22435-22674 Sentence denotes This indicated that even for the RT-qPCR–positive samples with a CT between 30 and 35, the color change that took place at time points > 30 min was caused by spurious amplification products and not by late amplification of viral sequences.
T187 22675-22876 Sentence denotes These results therefore confirmed that LAMP-sequencing was able to assess the results of multiple RT-LAMP reactions in parallel and to identify false-positive samples in the colorimetric RT-LAMP assay.
T188 22878-22923 Sentence denotes A swab–to–RT-LAMP assay without RNA isolation
T189 22924-23039 Sentence denotes RNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic.
T190 23040-23253 Sentence denotes 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.
T191 23254-23472 Sentence denotes 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.
T192 23473-23665 Sentence denotes 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.
T193 23666-23798 Sentence denotes We titrated defined numbers of IVT RNA molecules of the SARS-CoV-2 N gene into swab samples from COVID-19–negative control subjects.
T194 23799-23995 Sentence denotes 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.
T195 23996-24025 Sentence denotes S6 and S7, and data file S1).
T196 24026-24354 Sentence denotes 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.
T197 24356-24411 Sentence denotes Testing clinical samples with the swab–to–RT-LAMP assay
T198 24412-24629 Sentence denotes On the basis of these preliminary experiments, we decided to use swab samples either directly without any treatment (direct swab–to–RT-LAMP assay) or after heat treatment for 5 min at 95°C (hot swab–to–RT-LAMP assay).
T199 24630-24741 Sentence denotes As an additional precaution, we kept the samples in the cold (using an ice-cold metal block) whenever possible.
T200 24742-24849 Sentence denotes For testing large numbers of clinical samples, we performed the RT-LAMP assay using several 96-well plates.
T201 24850-25008 Sentence denotes In total, we tested 209 different samples using the hot swab–to–RT-LAMP assay, and of these, 131 samples also were tested by the direct swab–to–RT-LAMP assay.
T202 25009-25156 Sentence denotes Many samples were tested twice but using aliquots withdrawn at different time points (usually within 24 hours) from the swab samples stored at 4°C.
T203 25157-25277 Sentence denotes This resulted in 235 direct swab–to–RT-LAMP assay measurements and 343 hot swab–to–RT-LAMP assay measurements (Fig. 5A).
T204 25278-25520 Sentence denotes The hot swab–to–RT-LAMP assay detected a color change in the majority of samples with a CT < 30 with high sensitivity, whereas the direct swab–to–RT-LAMP assay only exhibited a high sensitivity for samples with a CT < 25 (Fig. 5 and Table 3).
T205 25521-25665 Sentence denotes The heat treatment rendered the RT-LAMP assay more stringent as it reduced false positives and more sensitive for samples with a CT of 25 to 30.
T206 25666-25770 Sentence denotes We found that some positive samples did not induce a color change but did so when assayed a second time.
T207 25771-25846 Sentence denotes We therefore would recommend running this assay using technical duplicates.
T208 25847-25913 Sentence denotes Fig. 5 Swab–to–RT-LAMP assay of clinical pharyngeal swab samples.
T209 25914-26087 Sentence denotes (A) Skipping a prior RNA isolation step, pharyngeal swab samples were subjected to the RT-LAMP assay either directly (left) or after 5 min of heat treatment at 95°C (right).
T210 26088-26226 Sentence denotes For each sample, scatter plots are used to compare the swab–to–RT-LAMP assay results (ΔOD values) with the results of RT-qPCR (CT values).
T211 26227-26499 Sentence denotes The measurement time point was 30 min after the start of the 65°C incubation. (B) Shown is the sensitivity (right) and specificity (left) of the swab–to–RT-LAMP assay [derived from the data in (A)] using the decision threshold indicated by the horizontal gray line in (A).
T212 26500-26741 Sentence denotes Specificity and sensitivity values (thick lines) are shown with their 95% confidence intervals (boxes) as in Fig. 3, with blue indicating the direct swab–to–RT-LAMP assay and red indicating the hot swab–to–RT-LAMP assay. (Also see table S3).
T213 26742-26856 Sentence denotes Table 3 Shown is RT-qPCR and RT-LAMP testing of 592 clinical samples stratified into CT value bins (see Fig. 5A).
T214 26857-26948 Sentence denotes Fig. 5A and table S3 show specificity and sensitivity values calculated from these numbers.
T215 26949-26979 Sentence denotes Hot swab–to–RT-LAMP RT-LAMP
T216 26980-27000 Sentence denotes CT Pos Neg Sum
T217 27001-27032 Sentence denotes RT-qPCR Pos 0–25 38 4 42
T218 27033-27049 Sentence denotes 25–30 17 5 22
T219 27050-27066 Sentence denotes 30–35 5 23 28
T220 27067-27083 Sentence denotes 35–40 0 36 36
T221 27084-27106 Sentence denotes Neg Neg 1 214 215
T222 27107-27124 Sentence denotes Sum 61 282 343
T223 27125-27158 Sentence denotes Direct swab–to–RT-LAMP RT-LAMP
T224 27159-27179 Sentence denotes CT Pos Neg Sum
T225 27180-27211 Sentence denotes RT-qPCR Pos 0–25 15 1 16
T226 27212-27228 Sentence denotes 25–30 6 11 17
T227 27229-27245 Sentence denotes 30–35 2 21 23
T228 27246-27262 Sentence denotes 35–40 3 23 26
T229 27263-27285 Sentence denotes Neg Neg 9 144 153
T230 27286-27303 Sentence denotes Sum 35 200 235
T231 27305-27362 Sentence denotes Heterogeneity of specimen pH in the swab–to–RT-LAMP assay
T232 27363-27573 Sentence denotes Comparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A).
T233 27574-27680 Sentence denotes This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction.
T234 27681-27767 Sentence denotes This might have affected the interpretability of the measurement at 30 min (ΔOD30min).
T235 27768-27831 Sentence denotes We investigated how this pH shift influenced the RT-LAMP assay.
T236 27832-27964 Sentence denotes For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A).
T237 27965-28147 Sentence denotes We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B).
T238 28148-28330 Sentence denotes This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.
T239 28331-28400 Sentence denotes Fig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.
T240 28401-28525 Sentence denotes (A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min.
T241 28526-28663 Sentence denotes Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay.
T242 28664-28724 Sentence denotes Also, the 40-min time point was not available for one plate.
T243 28725-28850 Sentence denotes The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes.
T244 28851-29152 Sentence denotes The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis.
T245 29153-29226 Sentence denotes The latter shows better separation between positive and negative samples.
T246 29227-29372 Sentence denotes We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs.
T247 29373-29538 Sentence denotes For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal.
T248 29539-29711 Sentence denotes Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay.
T249 29713-29723 Sentence denotes DISCUSSION
T250 29724-29830 Sentence denotes Here, we evaluated the use and suitability of the RT-LAMP assay for the detection of SARS-CoV-2 infection.
T251 29831-29969 Sentence denotes We also developed LAMP-sequencing as a fully scalable alternative to colorimetric or fluorometric analysis of DNA amplification reactions.
T252 29970-30181 Sentence denotes Our results indicate that whereas the RT-LAMP assay using the N-A primer set is not sensitive enough to replace RT-qPCR in all applications, it does hold promise as a method for testing large numbers of samples.
T253 30182-30345 Sentence denotes We tested the RT-LAMP primer sets suggested by Zhang et al. (11) and found that the N-A primer set for the N gene worked better than the 1a-A primer set for ORF1a.
T254 30346-30614 Sentence denotes For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens (Fig. 3 and Table 1).
T255 30615-30683 Sentence denotes For samples with CT > 30, the RT-LAMP assay was much less sensitive.
T256 30684-30801 Sentence denotes However, there is debate about which CT value for a positive RT-qPCR result should be considered clinically relevant.
T257 30802-30900 Sentence denotes Vogels et al. (16) indicate that a CT value above 36 corresponds to less than 10 molecules of RNA.
T258 30901-31067 Sentence denotes On the basis of our data, we conclude that the colorimetric RT-LAMP assay would be suitable for identifying individuals with a high or moderate SARS-CoV-2 viral load.
T259 31068-31327 Sentence denotes On the other hand, for those with a low viral load (at the onset of illness or during later stages of the disease), the sensitivity of the RT-LAMP assay, in its current implementation using the N-A primer set, is insufficient to detect a SARS-CoV-2 infection.
T260 31328-31589 Sentence denotes A number of other LAMP primer sets have been proposed and initially tested (21, 27, 28), showing that optimized primers and the use of combinations of primer sets hold promise to further increase the sensitivity of the RT-LAMP assay for detecting viral genomes.
T261 31590-31680 Sentence denotes Furthermore, alternative sample types, e.g., sputum or stool (29), might be more reliable.
T262 31681-31907 Sentence denotes One promising lead for future applications is the exploration of the hot swab–to–RT-LAMP assay using saliva specimens, although the relative sensitivity compared to using pharyngeal swab specimens is currently unclear (30–33).
T263 31908-32023 Sentence denotes Compatibility of the RT-LAMP assay with direct saliva specimens has been shown using spike-in experiments (22, 34).
T264 32024-32171 Sentence denotes Although faster and more convenient, the direct swab–to–RT-LAMP assay was less sensitive and less robust than the RT-LAMP assay using isolated RNA.
T265 32172-32434 Sentence denotes To increase robustness, various treatments of crude swab samples have been described previously [reviewed in (35)], many of which require additional processing of the samples, for example, by pipetting or by adding proteinase K to degrade contaminating proteins.
T266 32435-32652 Sentence denotes Rabe and Cepko (22) have suggested using cheap silica preparations and new sample inactivation protocols to enrich the RNA before the RT-LAMP assay, but this would complicate the simple swab–to–RT-LAMP assay workflow.
T267 32653-32908 Sentence denotes Last, our analysis found that a short heat treatment of 5 min at 95°C, which poses minimal additional handling steps, did not destroy the RNA but rather stabilized it and this improved the sensitivity and specificity of the swab–to–RT-LAMP assay (Fig. 5).
T268 32909-33054 Sentence denotes The heat likely helped to homogenize the sample, to inactivate ribonucleases (RNAses), and to break up the viral capsid to release the viral RNA.
T269 33055-33252 Sentence denotes Overall, our data demonstrate the feasibility of using a swab–to–RT-LAMP test and suggest applications especially in scenarios where RNA isolation is not available, e.g., in resource-poor settings.
T270 33253-33432 Sentence denotes In such cases, the hot swab–to–RT-LAMP assay seems a good option given that the direct swab–to–RT-LAMP assay yields a number of false positives due to spurious amplification (14).
T271 33433-33637 Sentence denotes Although spike-in experiments with IVT RNA can be informative, we have experienced clear differences when comparing such experiments to those using clinical RNA samples isolated from swab specimens (figs.
T272 33638-33667 Sentence denotes S6 and S7, and data file S1).
T273 33668-33843 Sentence denotes We therefore recommend validating any new proposed rapid SARS-CoV-2 diagnostic test using “real-life” clinical samples including a large fraction of negative clinical samples.
T274 33844-34028 Sentence denotes To overcome the problem of spurious amplification, an expanded oligonucleotide set that incorporates sequence-specific probes (34) or a CRISPR/Cas12a–based approach (36) could be used.
T275 34029-34126 Sentence denotes However, these applications have yet to be tested with large numbers of diverse clinical samples.
T276 34127-34195 Sentence denotes There are several differences between the RT-LAMP assay and RT-qPCR.
T277 34196-34425 Sentence denotes First, RT-qPCR requires a thermocycler to conduct the DNA amplification reaction, which is an expensive instrument, whereas isothermal incubation of RT-LAMP reactions can be conducted using a simple water bath or a heating block.
T278 34426-34500 Sentence denotes This makes the RT-LAMP assay more amenable for point-of-care applications.
T279 34501-34618 Sentence denotes Second, the reagents for the RT-LAMP assay are different from the ones used for RT-qPCR and are supplier independent.
T280 34619-34789 Sentence denotes According to the supplier of the RT-LAMP reagents used in this study (New England Biolabs), production of RT-LAMP reagents can be easily ramped up to satisfy high demand.
T281 34790-34964 Sentence denotes Third, the RT-LAMP assay, when combined with LAMP-sequencing, is suitable for analyzing large numbers of RT-LAMP reactions owing to the fully scalable DNA barcoding strategy.
T282 34965-35102 Sentence denotes In contrast, there are several hurdles to scaling up RT-qPCR assays, the major hurdle being the need for a large number of thermocyclers.
T283 35103-35206 Sentence denotes The RT-LAMP assay overcomes this problem and therefore will be a more scalable method for mass testing.
T284 35208-35273 Sentence denotes Application of RT-LAMP and LAMP-sequencing for SARS-CoV-2 testing
T285 35274-35381 Sentence denotes With its good sensitivity for samples up to CT ≈ 30, the colorimetric RT-LAMP assay has several advantages:
T286 35382-35453 Sentence denotes It is fast, inexpensive, and it can be evaluated without any equipment.
T287 35454-35702 Sentence denotes RT-LAMP reactions also appear to be less sensitive to contaminants in the samples than RT-qPCR, but care has to be taken that the samples used do not alter the pH as the colorimetric RT-LAMP assay is performed under conditions of weak pH buffering.
T288 35703-35867 Sentence denotes Some clinical samples contain contaminants that can lead to acidification of the reaction independent of the presence of a template RNA if too much sample is added.
T289 35868-36145 Sentence denotes Diagnostic RT-qPCR tests usually include a technical internal control, i.e., another RNA species, which is spiked into all samples and which is detected independent of the gene of interest to safeguard against the possibility of a general reaction failure within a sample tube.
T290 36146-36219 Sentence denotes It would be desirable to have a similar precaution for the RT-LAMP assay.
T291 36220-36348 Sentence denotes A multiplexed fluorescence readout might provide this (34) but comes at the expense of the simplicity of a colorimetric readout.
T292 36349-36643 Sentence denotes Our particular implementation of deep sequencing to analyze many RT-LAMP reactions simultaneously uses two sets of barcoded primers and is fully scalable so that, in one sequencing run, many thousands of LAMP reactions can be quantitatively analyzed for the presence of viral genomic sequences.
T293 36644-36830 Sentence denotes Although we used Illumina dye sequencing, more scalable sequencing technologies, such as Oxford Nanopore Technologies sequencing, could be used for amplicon sequencing and counting (37).
T294 36831-36975 Sentence denotes The workflow shown here uses LAMP-sequencing as a validation and backup procedure to double check the results of the colorimetric RT-LAMP assay.
T295 36976-37211 Sentence denotes However, LAMP-sequencing could also facilitate scale-up of the workflow for direct analysis of many thousands of samples in an efficient manner, provided that an infrastructure is established that allows the collection of such samples.
T296 37212-37319 Sentence denotes Thus, LAMP-sequencing could become an important part of workflows for routine testing of large populations.
T297 37320-37531 Sentence denotes Schmid-Burgk et al. (38) proposed decentralized RT-LAMP assays using combinatorial primer barcoding and centralized mass analysis of RT-LAMP products by next-generation sequencing as a means to scale-up testing.
T298 37532-37757 Sentence denotes Although this poses additional challenges in generating the individualized RT-LAMP assay reagents, it would simplify sample handling on the analytical side and it can be easily combined with the barcoding strategy shown here.
T299 37758-37801 Sentence denotes There are several limitations to our study.
T300 37802-37912 Sentence denotes We used surplus RNA sample material from a diagnostic laboratory rather than newly collected clinical samples.
T301 37913-38016 Sentence denotes The criteria for testing individuals may have influenced cohort characteristics and hence our findings.
T302 38017-38188 Sentence denotes It is not clear yet how well viral load as indicated by CT values from RT-qPCR assays informs about the degree of infectivity of an individual with a SARS-CoV-2 infection.
T303 38189-38400 Sentence denotes Therefore, we cannot say how our findings on the sensitivity of the RT-LAMP assay in comparison to RT-qPCR would translate into sensitivity for detecting infectious individuals who are shedding SARS-CoV-2 virus.
T304 38401-38601 Sentence denotes Moreover, the measured viral load does not indicate the course of a SARS-CoV-2 infection, as even individuals with a very low measured viral load can still develop severe symptoms of COVID-19 disease.
T305 38602-38801 Sentence denotes This may be, in part, because the viral load in a clinical sample taken from a specific site such as the pharynx is not representative of the overall viral burden that an infected individual carries.
T306 38802-38904 Sentence denotes We used LAMP-sequencing to validate the RT-LAMP assay results and did not use it as a diagnostic tool.
T307 38905-39082 Sentence denotes LAMP-sequencing is dependent on the sensitivity of the RT-LAMP reaction as it cannot detect false negative results caused by a failure of the RT-LAMP assay to amplify viral RNA.
T308 39083-39204 Sentence denotes Also, reagents such as the primer sets for the RT-LAMP assay may be subject to production-dependent quality fluctuations.
T309 39205-39318 Sentence denotes Therefore, all reagents must be precisely validated (batch control) before using an RT-LAMP assay diagnostically.
T310 39319-39433 Sentence denotes Application of the RT-LAMP assay has great potential, even more so as more sensitive primer sets become available.
T311 39434-39574 Sentence denotes The RT-LAMP assay and LAMP-sequencing could offer scalable testing that would be difficult to achieve with conventional RT-qPCR–based tests.
T312 39575-39773 Sentence denotes For example, the RT-LAMP assay could be used for regular testing of a whole workforce or in sentinel testing, ideally combined with simplified sample collection, e.g., in the form of saliva samples.
T313 39774-39998 Sentence denotes The RT-LAMP assay and LAMP-sequencing extend the range of available test methods and complement individual tests and pooled tests based on RT-qPCR (39) with a faster, simpler, and potentially more cost-effective test method.
T314 40000-40021 Sentence denotes MATERIALS AND METHODS
T315 40023-40035 Sentence denotes Study design
T316 40036-40221 Sentence denotes The intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19.
T317 40222-40433 Sentence denotes We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital.
T318 40434-40640 Sentence denotes Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question.
T319 40641-40815 Sentence denotes Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.
T320 40816-41069 Sentence denotes Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens.
T321 41070-41145 Sentence denotes This study was conducted in Heidelberg, Germany in March and April of 2020.
T322 41146-41424 Sentence denotes The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation.
T323 41425-41699 Sentence denotes All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay.
T324 41700-41849 Sentence denotes The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result.
T325 41850-42029 Sentence denotes We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing).
T326 42031-42055 Sentence denotes Clinical sample handling
T327 42056-42169 Sentence denotes Specimens were collected as nasopharyngeal and oropharyngeal flocked swabs in Amies medium (eSwab, Copan Italia).
T328 42170-42342 Sentence denotes The sample collection happened as part of the routine operation of Heidelberg University Hospital and at public testing stations set up by the City of Heidelberg (fig. S1).
T329 42343-42529 Sentence denotes Collected samples were transported in sterile containers, delivered to the diagnostic laboratory within a few hours, and then examined directly or stored at 4°C until further processing.
T330 42530-42641 Sentence denotes Samples were processed in a biosafety level 2 cabinet until inactivation by heat or mixing with a lysis buffer.
T331 42643-42668 Sentence denotes RNA isolation and RT-qPCR
T332 42669-43016 Sentence denotes The standard diagnostic pipeline of the hospital laboratory was as follows: RNA was isolated from nasopharyngeal and oropharyngeal swab specimens using QIAGEN kits (QIAGEN, Hilden, Germany); either automated on the QIASymphony (DSP Virus/Pathogen Mini Kits) or QIAcube (QIAamp Viral RNA Mini Kits) devices or manually (QIAamp Viral RNA Mini Kits).
T333 43017-43197 Sentence denotes Please note that the QiaCube uses a sample volume of 140 μl and an elution volume of 100 μl, whereas the QiaSymphony uses a sample volume of 200 μl and an elution volume of 115 μl.
T334 43198-43345 Sentence denotes RT-qPCR for the quantification of the SARS-CoV-2 viral genome was performed using kits and reagents from TIB MOLBIO Syntheselabor, Berlin, Germany.
T335 43346-43502 Sentence denotes The kits were used according to the manufacturer’s instruction and contained the primer/probe sets developed based on the published Sarbeco primer set (15).
T336 43503-43716 Sentence denotes Per 20-μl reaction, the master mix contained 5.4 μl of RNAse free water, 4.0 μl of LightCycler Multiplex RNA Virus Master (Roche, Basel, Switzerland), 0.5 μl of LightMix Modular SARS and Wuhan CoV E gene (cat. no.
T337 43717-43833 Sentence denotes 53-0776-96; TIB MOLBIOL Syntheselabor GmbH, Berlin, Germany) or LightMix Modular SARS and Wuhan CoV N gene (cat. no.
T338 43834-43923 Sentence denotes 53-0775-96; TIB MOLBIOL), 0.5 μl of LightMix Modular EAV RNA Extraction Control (cat. no.
T339 43924-44061 Sentence denotes 66-0909-96; TIB MOLBIOL), and 0.1 μl of reverse transcriptase enzyme (LightCycler Multiplex RNA Virus Master, Roche, Basel, Switzerland).
T340 44062-44180 Sentence denotes The master mix (10 μl) was distributed per reaction into 96-well plates, and 10 μl of purified RNA was added per well.
T341 44181-44266 Sentence denotes The performance of the RT-qPCR was validated using a positive control for the E gene.
T342 44267-44351 Sentence denotes A total of 103 molecules of E gene RNA per RT-qPCR reaction correspond to a CT ≈ 30.
T343 44353-44395 Sentence denotes RT-LAMP primer design and positive control
T344 44396-44611 Sentence denotes The RT-LAMP primer sets used in this study have been designed by Zhang et al. (11) against ORF1a and N gene and were synthesized by Sigma-Aldrich (synthesis scale, 0.025 μmol; purification, desalt; solution, water).
T345 44612-44747 Sentence denotes The sequences and the concentrations of each oligonucleotide in the 10× primer mix used for the RT-LAMP assay can be found in table S1.
T346 44748-45121 Sentence denotes An RNA-positive control for the N gene was amplified from a short fragment from 2019-nCoV_N_Positive control plasmid [Integrated DNA Technologies (IDT), 10006625] with oligonucleotides T7-GeneN-Fragment.for and GeneN-Fragment.rev including the T7 promoter and a subsequent IVT with the MEGAscript T7 Kit (Invitrogen) purified using the RNeasy MinElute Cleanup Kit (QIAGEN).
T347 45123-45206 Sentence denotes Liquid handling using 96-well plates and precautions taken to prevent contamination
T348 45207-45273 Sentence denotes To prevent cross-contamination, we have taken several precautions.
T349 45274-45380 Sentence denotes The 10× primer mix was prepared with nuclease-free water (AM9937, Ambion) and stored in aliquots at −20°C.
T350 45381-45549 Sentence denotes To set up an RT-LAMP test, the RT-LAMP master mix was prepared freshly immediately before the test at a separate workspace with a dedicated pipette set and filter tips.
T351 45550-45670 Sentence denotes The 96-well PCR plate containing the RT-LAMP mix was covered with an Society for Biomolecular Screening (SBS) plate lid.
T352 45671-45816 Sentence denotes To avoid mix-ups during sample addition through well-by-well pipetting, the RNA or swab specimens were first collected into a 96-well seed plate.
T353 45817-45988 Sentence denotes The RNA was then added to the plate with the LAMP reagents at a dedicated workspace with a manual 96-channel pipettor (Liquidator 20 μl, Mettler Toledo) using filter tips.
T354 45989-46208 Sentence denotes The RT-LAMP and the RNA seed plate were instantly sealed with an optically clear adhesive seal (GK480-OS, Kisker Biotech) and an adhesive aluminum foil seal (SL-AM0550, Steinbrenner Laborsysteme, Germany), respectively.
T355 46209-46423 Sentence denotes If the product of an RT-LAMP reaction had to be analyzed by gel electrophoresis, the plate was opened with extreme caution at a separated post-LAMP workspace and loaded onto an agarose gel with a dedicated pipette.
T356 46425-46438 Sentence denotes RT-LAMP assay
T357 46439-46580 Sentence denotes Assays were assembled in total reaction volumes of either 12.5 μl (for LAMP assays using isolated RNA) or 20 μl (for swab–to–RT-LAMP assays).
T358 46581-46915 Sentence denotes Master mixes were prepared at room temperature for each reaction immediately before use with either 6.25 or 10 μl, respectively, of the WarmStart Colorimetric RT-LAMP 2X Master Mix (M1800, New England Biolabs) and 1.25 or 2 μl, respectively, of the 10× primer mix, filled up to 11.5 or 19 μl with nuclease-free water (AM9937, Ambion).
T359 46916-46950 Sentence denotes Values given are for one reaction:
T360 46951-47230 Sentence denotes For a 96-well plate, 100 times larger volumes were used, and the LAMP mix was distributed to the wells of a 96-well plate (4ti-0960/C, Brooks Life Sciences or 0030128672, Eppendorf) before pipetting 1 μl of sample into each well of the plate; for details, see previous paragraph.
T361 47231-47412 Sentence denotes Plates were prepared immediately before use to limit exposure of the LAMP reagents to atmospheric CO2 (to prevent acidification of the reaction) and kept on an ice-cold metal block.
T362 47413-47596 Sentence denotes Plates were sealed using a transparent adhesive foil (GK480-OS, Kisker Biotech), and the reactions were incubated in a PCR cycler at 65°C for 15 to 60 min with the lid heated to 75°C.
T363 47597-47747 Sentence denotes To perform measurements at the indicated time points, the reactions were taken out of the PCR cycler and placed into an ice cold metal block for 30 s.
T364 47748-47798 Sentence denotes This intensifies the color before the measurement.
T365 47799-47899 Sentence denotes Photographs were taken with cell phone cameras or the scanner function of an office copying machine.
T366 47901-47939 Sentence denotes Quantification of the RT-LAMP reaction
T367 47940-48056 Sentence denotes Absorbance measurements were performed with a Spark Cyto or Infinite M200 (Tecan) at 434 and 560 nm with 25 flashes.
T368 48057-48217 Sentence denotes These two peaks from phenol red are strongly changing during the acidification of the reaction (434 nm absorbance is increased, 560 nm absorbance is decreased).
T369 48218-48324 Sentence denotes To obtain a good readout of the color change, absorbance at 560 nm was substracted from the one at 434 nm.
T370 48325-48357 Sentence denotes This difference was denoted ΔOD.
T371 48359-48380 Sentence denotes Swab–to–RT-LAMP assay
T372 48381-48496 Sentence denotes For direct and hot swab–to–RT-LAMP assays, patient swab specimens were transferred first onto a 96-well seed plate.
T373 48497-48657 Sentence denotes For the direct assay, we then transferred 1 μl of the specimen directly to 19 μl of LAMP mix per well in a ready-made 96-well PCR plate (0030128672, Eppendorf).
T374 48658-48776 Sentence denotes The plate was sealed using a transparent adhesive foil (GK480-OS, Kisker Biotech) and kept on an ice-cold metal block.
T375 48777-48958 Sentence denotes For the hot assay, we sealed the seed plate with a pierceable lid (4ti-0566/96, Brooks Life Sciences) and heated it in a PCR cycler for 5 min at 95°C (with the lid heated to 105°C).
T376 48959-49024 Sentence denotes The seed plate was cooled down to 4°C on an ice-cold metal block.
T377 49025-49158 Sentence denotes Afterward, 1 μl of the heat-treated patient specimens was quickly added to a second ready-made plate with 19 μl of LAMP mix per well.
T378 49159-49244 Sentence denotes This plate was also sealed with transparent adhesive foil (GK480-OS, Kisker Biotech).
T379 49245-49318 Sentence denotes Both plates were then incubated at 65°C for the LAMP reaction to proceed.
T380 49319-49480 Sentence denotes For both swab–to–RT-LAMP assays, the PCR plates were briefly spun down and then incubated in a PCR cycler at 65°C for 10 to 60 min (with the lid heated to 75°C).
T381 49481-49631 Sentence denotes To perform measurements at the indicated time points, the reactions were taken out of the PCR cycler and placed into an ice-cold metal block for 30 s.
T382 49633-49655 Sentence denotes LAMP-sequencing method
T383 49656-49876 Sentence denotes Sequencing libraries for detecting viral sequences in RT-LAMP products were prepared by a modified Anchor-Seq protocol (37, 40) using Tn5 transposase tagmentation instead of sonication for genomic DNA fragmentation (17).
T384 49877-49925 Sentence denotes The relevant primers are summarized in table S4.
T385 49926-50233 Sentence denotes In detail, transposon adapters containing well-defining barcodes and unique molecular identifiers (UMIs) were annealed by mixing 25 μM oligos (P5-UMI-xi5001…5096-ME.fw, Tn5hY-Rd2-Wat-SC3) in 5 μM tris-HCl (pH 8), incubating at 99°C for 5 min, and slowly cooling down to 20°C within 15 min in a thermocycler.
T386 50234-50446 Sentence denotes Transposons were assembled by mixing Tn5(E54K, L372P) transposase (100 ng/μl) [purified according to (41)] with 1.25 μM annealed adapters in 50 mM Tris-HCl (pH 7.5) and incubating the reaction for 1 hour at 23°C.
T387 50447-50791 Sentence denotes Tagmentation was carried out by mixing 1.2 μl of the RT-LAMP product (~200 ng DNA) with 1.5 μl of loaded transposase in freshly prepared tagmentation buffer [10 mM [tris(hydroxymethyl)methylamino]propanesulfonic acid) (TAPS)] (pH 8.5), 5 mM MgCl2, and 10% (v/v) dimethylformamide] using a Liquidator 96 Manual Pipetting System (Mettler Toledo).
T388 50792-50840 Sentence denotes The reactions were incubated at 55°C for 10 min.
T389 50841-50913 Sentence denotes Reactions were stopped by adding SDS to a final concentration of 0.033%.
T390 50914-51080 Sentence denotes Tagmented DNA of each plate was pooled and size-selected using a two-step AMPureXP bead (Beckman Coulter) purification to target for fragments between 300 and 600 bp.
T391 51081-51197 Sentence denotes First, 50 μl of pooled reaction was mixed with 50 μl of water and bound to 55 μl of beads to remove large fragments.
T392 51198-51427 Sentence denotes To further remove small fragments, the supernatant of this reaction was added to 25 μl of fresh beads and further purified using two washes with 80% ethanol before the samples were finally eluted in 10 μl of 5 mM tris-HCl (pH 8).
T393 51428-51822 Sentence denotes One PCR per plate with 1 μl of the eluate and RT-LAMP–specific and Tn5-adapter–specific primers (P7nxt-GeneN-A-LBrc and P7-xi7001..7016, P5.fw) was performed using NEBNext Q5 HotStart polymerase (New England Biolabs) with two cycles at 62°C for annealing and 90 s elongation, followed by two cycles at 65°C for annealing and 90 s elongation, and 13 cycles at 72°C annealing and 90 s elongation.
T394 51823-51994 Sentence denotes All PCR reactions were combined and 19% of this pool was size-selected for 400 to 550 bp using a 2% agarose/tris-acetate-EDTA gel and column purification (Macherey-Nagel).
T395 51995-52335 Sentence denotes The final sequencing library was quantified by qPCR (New England Biolabs) and sequenced with a paired-end sequencing run on a NextSeq 550 machine (Illumina) with 20% phiX spike-in and 136 cycles for the first read, 11 cycles to read the 11-nt-long plate index (i7) and 20 cycles to read the 11-nt-long well index (i5) and the 9-nt-long UMI.
T396 52336-52449 Sentence denotes For trimming of the reads (i.e., removal of P7 Illumina adapter sequences), cutadapt (version 2.8) (42) was used.
T397 52450-52586 Sentence denotes For validation of the origin of the sequence of the LAMP product (fig. S4A), 107 reads were randomly selected and used for the analysis.
T398 52587-52724 Sentence denotes Reads were mapped to the SARS-CoV-2 reference genome (NC_045512.2) (43), using bwa-mem with default settings (version 0.7.17-r1188) (44).
T399 52725-52814 Sentence denotes Virus genome coverage was determined with the samtools depth command (version 1.10) (45).
T400 52815-52900 Sentence denotes Using bwa-mem, 80.6% of reads could be mapped to the virus genome (fig. S4, B and C).
T401 52901-52990 Sentence denotes To analyze the remaining sequences, a k-mer analysis using a custom script was performed.
T402 52991-53166 Sentence denotes Using 9-mers, this matched 93.5% of the nonmapped reads with a maximal Levenshtein distance of two to one of the LAMP primers or their reverse complement sequences (fig. S4D).
T403 53167-53263 Sentence denotes This is explained by the fact that LAMP products can consist of complex sequence rearrangements.
T404 53264-53376 Sentence denotes For classification of samples by LAMP-sequencing, reads were assigned to wells and counted using custom scripts.
T405 53377-53600 Sentence denotes A read was considered as a match to SARS-CoV-2 N gene if at least one of three short sequences (~13 nt, marked orange in fig. S4A) not covered by RT-LAMP primers was found in the read, otherwise it was counted as unmatched.
T406 53601-53718 Sentence denotes Sequencing reads were grouped by UMI and by position of the matched sequence with the aim of removing PCR duplicates.
T407 53719-53859 Sentence denotes A sample was considered if more than 200 total UMIs were observed and called positive if more than 10,000 virus-matching UMIs were observed.
T408 53860-53972 Sentence denotes There is a very wide gap in the number of virus-matching reads between positive and negative samples (fig. S5A):
T409 53973-54030 Sentence denotes The count is either below 7000 UMIs or above 45,000 UMIs.
T410 54031-54141 Sentence denotes This is why we placed the decision threshold for scoring a sample as LAMP-sequencing positive within this gap.
T411 54142-54431 Sentence denotes The fact that also RT-qPCR–negative samples give rise to some UMI counts containing viral sequences is explained by template switching of unattached adapters that remain in the reaction after tagmentation, but no cause for concern due to the wide gap between negative and positive samples.
T412 54432-54578 Sentence denotes For a few samples, we saw so few reads (less than 200 UMIs) that we suspected that the multiplexing had failed and excluded them from the results.
T413 54579-54757 Sentence denotes As most of these were in the same row of the same plate, we analyzed these samples after LAMP-sequencing by gel electrophoresis (fig. S5B) to check for DNA content after RT-LAMP.
T414 54758-54902 Sentence denotes We found that the gel results agree with the RT-LAMP outcome, indicating that the failure likely was caused later, probably during multiplexing.
T415 54904-54924 Sentence denotes Statistical analysis
T416 54925-55062 Sentence denotes Except where otherwise noted, all data were analyzed with R (46) using the tidyverse (47) and ggplot2 (48) system or with GraphPad Prism.
T417 55063-55141 Sentence denotes Sensitivity and specificity values were obtained from count tables as follows:
T418 55142-55279 Sentence denotes Specificity of the RT-LAMP assay was calculated as the fraction of RT-qPCR–negative samples that were also negative in the RT-LAMP assay.
T419 55280-55443 Sentence denotes Sensitivity for a given CT interval was calculated as the fraction of all samples with an RT-qPCR CT value in that interval that was positive in the RT-LAMP assay.
T420 55444-55666 Sentence denotes In both cases, 95% confidence intervals were calculated by interpreting the fractions of counts as binomial rates and then using Wilson’s method for binomial confidence intervals as implemented in the R package binom (49).
T421 55667-55831 Sentence denotes The R code used to perform analyses and produce figures can be found on GitHub, together with all data tables: https://github.com/anders-biostat/LAMP-Paper-Figures.