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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 74-77 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 125-128 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T3 181-184 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 281-284 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 727-730 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 964-967 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T7 1100-1103 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 1520-1523 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 1963-1966 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 2005-2009 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 2050-2053 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 2258-2261 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 2383-2386 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 2571-2574 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 4209-4215 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T16 4421-4424 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 4510-4513 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 4771-4774 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 4812-4818 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T20 4914-4917 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 4923-4926 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T22 4959-4962 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T23 5088-5094 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T24 5750-5753 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 5856-5859 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 5897-5904 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T27 6080-6083 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T28 6190-6193 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T29 6484-6487 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T30 6519-6522 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T31 6537-6541 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T32 6613-6616 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T33 6654-6657 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 6828-6831 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T35 7269-7272 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T36 7373-7376 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T37 7429-7432 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38 7533-7536 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T39 7606-7619 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T40 7606-7609 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41 7666-7669 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T42 7756-7759 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T43 8633-8636 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T44 8649-8652 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 8873-8876 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T46 9027-9030 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T47 9071-9074 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T48 9540-9543 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T49 9574-9577 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T50 9650-9653 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T51 9658-9661 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 10145-10148 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T53 10268-10271 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T54 10326-10329 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T55 10357-10363 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T56 10393-10397 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T57 10525-10529 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 10563-10576 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T59 10563-10566 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T60 10609-10612 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 11065-11068 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 11184-11187 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T63 11239-11252 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T64 11239-11242 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T65 11273-11277 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T66 11772-11785 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T67 11772-11775 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T68 11888-11891 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T69 12081-12084 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T70 12152-12155 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T71 12995-12999 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T72 13045-13048 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T73 13212-13215 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T74 13657-13661 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T75 15242-15255 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T76 15242-15245 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T77 15486-15489 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T78 15645-15658 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T79 15645-15648 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T80 15805-15808 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81 15812-15815 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T82 16051-16055 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T83 16099-16103 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T84 16232-16236 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 16357-16361 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T86 16368-16372 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T87 16487-16491 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 16531-16535 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T89 16569-16572 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T90 16678-16682 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T91 16868-16872 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T92 16950-16954 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T93 17224-17227 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T94 17334-17337 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T95 17373-17376 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T96 17742-17745 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T97 17856-17859 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T98 17901-17904 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 18635-18639 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T100 19581-19584 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T101 19876-19879 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T102 21111-21114 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T103 21654-21657 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T104 22447-22451 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T105 22469-22473 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T106 22577-22580 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T107 23017-23021 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T108 23095-23099 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T109 23235-23241 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T110 23580-23583 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T111 25788-25791 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T112 25802-25805 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T113 25959-25962 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T114 26314-26317 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T115 26485-26488 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T116 26579-26592 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T117 26579-26582 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T118 26613-26617 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T119 26830-26833 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T120 26949-26952 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T121 27186-27189 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T122 28813-28816 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T123 30341-30344 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T124 31864-31868 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T125 32025-32029 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T126 32819-32822 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T127 33169-33173 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T128 33378-33381 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T129 33419-33422 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T130 33774-33777 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T131 33959-33963 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T132 34459-34466 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T133 34513-34519 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T134 34523-34528 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T135 34660-34666 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T136 34833-34839 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T137 35045-35048 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T138 35303-35311 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 35432-35435 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T140 35669-35672 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T141 35928-35931 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T142 36066-36069 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T143 36350-36353 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T144 36468-36471 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T145 37128-37131 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T146 37819-37822 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T147 38713-38716 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T148 38831-38834 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T149 38918-38922 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T150 40696-40699 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T151 41585-41592 Body_part denotes pharynx http://purl.org/sig/ont/fma/fma46688
T152 41956-41959 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T153 42636-42642 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T154 42997-43000 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T155 43004-43007 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T156 43134-43137 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T157 43594-43598 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472
T158 43623-43628 Body_part denotes mouth http://purl.org/sig/ont/fma/fma49184
T159 43896-43899 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T160 43903-43906 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T161 44166-44169 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T162 44173-44176 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T163 44241-44244 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T164 44288-44291 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T165 44307-44310 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T166 44457-44460 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T167 45521-45524 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T168 45623-45626 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T169 45830-45833 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T170 45879-45882 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T171 46131-46137 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T172 46486-46489 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T173 46580-46584 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T174 46697-46701 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T175 46769-46772 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T176 46894-46897 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T177 47035-47038 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T178 47139-47143 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T179 47175-47179 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T180 47180-47183 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T181 47377-47381 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T182 47629-47632 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T183 47660-47664 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T184 47755-47758 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T185 48625-48628 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T186 48699-48702 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T187 48887-48890 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T188 49415-49418 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T189 50705-50709 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T190 52731-52734 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T191 53403-53406 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T192 53802-53805 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T193 55511-55517 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T194 55609-55615 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T195 55752-55758 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T196 56304-56308 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T197 57609-57612 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T198 58952-58955 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T199 61976-61979 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T200 62069-62072 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 935-940 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T2 3663-3668 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 33959-33963 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T4 34513-34519 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 34523-34528 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T6 34660-34666 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T7 34833-34839 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T8 39018-39022 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T9 39901-39906 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T10 40392-40397 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T11 41585-41592 Body_part denotes pharynx http://purl.obolibrary.org/obo/UBERON_0006562
T12 42636-42642 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T13 43594-43598 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004
T14 43623-43628 Body_part denotes mouth http://purl.obolibrary.org/obo/UBERON_0000165
T15 47431-47436 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 63-71 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 170-178 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 270-278 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 362-371 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 381-389 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 814-822 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 953-961 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1227-1251 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T9 1253-1261 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1286-1294 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 1298-1345 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1298-1331 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T13 1430-1438 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 1441-1451 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T15 1946-1954 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2150-2158 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 2241-2249 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 2372-2380 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 2895-2919 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T20 2921-2929 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 2955-2963 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2967-3014 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T23 2967-3000 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T24 3205-3213 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 3373-3381 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 3384-3393 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T27 3463-3471 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 3540-3549 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T29 3882-3891 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T30 4141-4149 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 4152-4161 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T32 4285-4293 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 4499-4507 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 4556-4564 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 5502-5510 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 5739-5747 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 7290-7299 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 7418-7426 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 7655-7663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 8485-8493 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 8622-8630 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 8745-8753 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 8862-8870 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 9529-9537 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 9563-9571 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 10134-10142 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 10346-10354 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 11260-11268 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 11761-11769 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 12415-12417 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T51 12637-12639 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T52 13644-13652 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 13781-13783 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T54 13940-13942 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T55 14001-14003 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T56 14215-14217 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T57 14700-14702 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T58 14786-14788 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T59 16558-16566 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 17213-17221 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 17731-17739 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 19497-19499 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T63 19570-19578 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 19865-19873 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 20223-20225 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T66 22566-22574 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 26600-26608 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 26641-26649 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T69 27175-27183 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 29053-29055 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T71 30390-30392 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T72 30873-30875 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T73 31311-31313 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T74 31456-31458 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T75 31832-31834 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T76 31944-31946 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T77 32687-32695 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 32698-32707 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 33367-33375 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 33923-33931 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 34184-34192 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 34195-34204 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 36603-36611 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 38133-38141 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 41045-41053 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 41056-41065 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 41221-41231 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T88 41261-41269 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T89 41347-41355 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 41358-41367 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 41462-41470 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T92 42986-42994 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 43090-43098 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T94 43204-43212 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T95 43215-43224 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T96 43879-43887 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 44155-44163 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 44230-44238 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 45259-45266 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T100 46114-46122 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 46559-46563 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T102 46676-46680 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T103 48533-48536 Disease denotes SBS http://purl.obolibrary.org/obo/MONDO_0011526
T104 51232-51234 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T105 55490-55498 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 56291-56299 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T107 59036-59044 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 62127-62135 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 99-100 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T3 250-251 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T4 261-265 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T5 329-333 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T6 525-540 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumentation
T7 674-680 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T8 803-809 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T9 866-867 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 941-948 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T11 1004-1005 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1092-1093 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1130-1131 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1362-1363 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1401-1406 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T16 1466-1471 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 1663-1670 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T18 1796-1797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1864-1879 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumentation
T20 1890-1896 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T21 1897-1898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1973-1974 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2005-2009 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T24 2014-2020 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T25 2139-2145 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T26 2298-2299 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 2449-2450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2476-2477 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 2518-2519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 2563-2564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 2733-2734 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 2788-2789 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 3036-3037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3066-3067 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35 3186-3187 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 3230-3231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 3306-3313 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T38 3362-3368 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T39 3507-3512 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T40 3514-3518 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T41 3569-3577 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T42 3632-3637 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 3730-3735 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T44 3930-3937 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T45 3961-3962 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 3993-3994 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 4134-4140 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T48 4249-4254 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 4526-4533 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T50 4592-4595 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T51 4655-4659 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T52 4852-4853 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 4940-4941 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 5051-5052 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 5061-5062 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5141-5142 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5183-5190 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T58 5196-5197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 5319-5320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 5454-5458 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T61 5689-5693 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T62 6050-6051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 6078-6079 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 6127-6135 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T65 6214-6215 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 6340-6341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 6648-6649 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 6678-6679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 6928-6929 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 6986-6987 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 7085-7086 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 7273-7280 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 7300-7305 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 7556-7557 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 7671-7672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 7694-7699 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T77 7865-7866 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 7960-7961 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 8014-8018 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T80 8117-8118 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 8218-8219 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 8537-8543 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T83 8579-8580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 8734-8740 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T85 8877-8884 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T86 8903-8905 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T87 8926-8927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 9050-9056 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T89 9088-9089 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 9228-9229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 9766-9767 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 10166-10168 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T93 10289-10295 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T94 10371-10372 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T95 10393-10397 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T96 10409-10410 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 10460-10462 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T98 10465-10467 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T99 10525-10529 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T100 10580-10581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 10582-10586 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T102 10748-10750 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T103 10877-10878 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 11190-11191 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 11273-11277 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T106 11584-11585 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T107 11641-11644 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T108 11641-11644 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T109 11687-11688 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 11822-11823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 11871-11878 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T112 12036-12037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 12159-12160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 12201-12202 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 12233-12235 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T116 12316-12318 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T117 12355-12356 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 12554-12555 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 12792-12796 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 12863-12871 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T121 12888-12889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 12912-12916 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T123 12932-12933 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 12995-12999 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T125 13308-13309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 13458-13459 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T127 13499-13500 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T128 13539-13540 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T129 13566-13567 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 13626-13627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 13657-13661 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T132 13675-13676 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 13691-13692 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T134 13998-13999 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 14256-14257 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T136 14329-14330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 14384-14385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 14488-14489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 14559-14561 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T140 14587-14588 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 14737-14738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 14883-14884 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 14900-14901 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 14937-14941 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T145 14993-14995 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T146 14997-14998 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 15079-15080 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 15148-15149 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 15211-15212 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 15431-15432 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 15549-15550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 15726-15727 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 16024-16030 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T154 16051-16055 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T155 16070-16071 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 16099-16103 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T157 16232-16236 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T158 16261-16262 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 16297-16299 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T160 16357-16361 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T161 16368-16372 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T162 16410-16411 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T163 16487-16491 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T164 16531-16535 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T165 16678-16682 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T166 16755-16761 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T167 16769-16770 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 16806-16808 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T169 16868-16872 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T170 16895-16896 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 16950-16954 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T172 17047-17048 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T173 17358-17359 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 17418-17420 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T175 17560-17561 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 17571-17574 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T177 17583-17587 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T178 17772-17773 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T179 17794-17795 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 17868-17874 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T181 17937-17938 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 17977-17978 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 18293-18294 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T184 18383-18384 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T185 18640-18646 http://purl.obolibrary.org/obo/CLO_0007225 denotes labels
T186 18779-18780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 19056-19058 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T188 19056-19058 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T189 19099-19106 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T190 19194-19196 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T191 19194-19196 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T192 19348-19350 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T193 19362-19364 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T194 19481-19482 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 19510-19511 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 19626-19627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 19781-19783 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T198 19908-19909 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 20281-20289 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T200 20482-20484 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T201 20482-20484 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T202 20654-20655 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 21175-21176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T204 21423-21424 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T205 21792-21793 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T206 21834-21835 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T207 21929-21931 http://purl.obolibrary.org/obo/CLO_0007653 denotes ME
T208 21945-21946 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 22288-22289 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T210 22511-22512 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 22820-22821 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T212 23149-23150 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T213 23954-23955 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T214 23967-23969 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T215 24116-24117 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T216 24174-24175 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 24753-24755 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T218 24765-24767 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T219 24845-24849 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T220 24853-24855 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T221 24867-24869 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T222 24971-24973 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T223 24983-24985 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T224 25099-25100 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T225 25212-25213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T226 25308-25310 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4C
T227 25376-25377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T228 25396-25398 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T229 25756-25757 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T230 25906-25907 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T231 26177-26179 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T232 26208-26210 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T233 26239-26246 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T234 26306-26307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T235 26392-26396 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T236 26613-26617 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T237 26680-26686 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T238 26768-26773 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T239 26860-26865 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T240 26899-26901 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T241 26953-26960 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T242 26973-26978 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T243 27234-27241 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T244 27624-27631 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T245 27741-27747 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T246 27843-27849 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T247 27905-27911 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T248 28030-28033 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T249 28195-28196 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T250 28242-28243 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T251 28331-28332 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T252 28367-28368 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 28526-28527 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 28595-28596 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T255 28634-28635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T256 28793-28794 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T257 28805-28806 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T258 29184-29185 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T259 29299-29300 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T260 29374-29375 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T261 29658-29665 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T262 29925-29927 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T263 29931-29933 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T264 29945-29947 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T265 29955-29957 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T266 29959-29961 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T267 30084-30089 http://purl.obolibrary.org/obo/CLO_0001046 denotes 1 16
T268 30100-30102 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T269 30110-30112 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T270 30124-30126 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T271 30169-30171 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T272 30354-30355 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T273 30475-30476 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T274 31146-31147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T275 31280-31281 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T276 31655-31656 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T277 31691-31692 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T278 31947-31954 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T279 32380-32381 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T280 32746-32747 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T281 32912-32913 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T282 33013-33014 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T283 33026-33033 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T284 33063-33069 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T285 33121-33123 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T286 33146-33147 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T287 33169-33173 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T288 33200-33201 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T289 33241-33242 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T290 33612-33613 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T291 33713-33714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T292 33730-33732 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T293 33904-33905 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T294 33980-33981 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T295 34142-34143 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T296 34182-34183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T297 34206-34207 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T298 34274-34280 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T299 34286-34288 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T300 34850-34853 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T301 34893-34895 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T302 34897-34899 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T303 35160-35162 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T304 35329-35331 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T305 35561-35562 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T306 35988-35989 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T307 36006-36010 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T308 36182-36183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T309 36247-36248 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T310 36541-36543 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T311 36625-36629 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T312 36675-36676 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T313 36849-36851 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T314 36856-36857 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T315 36888-36890 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T316 36950-36956 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T317 37098-37099 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T318 37178-37188 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T319 37264-37265 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T320 37287-37288 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T321 37948-37949 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T322 38044-38045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T323 38076-38083 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T324 38144-38151 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T325 38236-38239 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T326 38437-38440 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T327 38702-38703 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T328 38765-38770 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T329 38787-38788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 38918-38922 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T331 38975-38976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 39009-39010 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T333 39018-39022 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T334 39054-39055 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T335 39098-39099 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T336 39153-39155 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T337 39203-39204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T338 39757-39758 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T339 40168-40175 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T340 40381-40382 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T341 40401-40408 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T342 40721-40722 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 40808-40815 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T344 41043-41044 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 41272-41277 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T346 41345-41346 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T347 41394-41395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T348 41528-41529 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T349 41557-41558 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T350 41585-41592 http://purl.obolibrary.org/obo/UBERON_0001042 denotes pharynx
T351 41585-41592 http://purl.obolibrary.org/obo/UBERON_0006562 denotes pharynx
T352 41764-41765 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T353 41908-41909 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 42230-42233 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T355 42371-42378 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T356 42446-42451 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T357 42510-42517 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T358 42521-42522 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T359 42554-42561 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T360 42720-42724 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T361 42759-42764 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T362 42776-42781 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T363 42809-42810 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 42864-42868 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T365 42954-42955 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T366 43079-43085 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T367 43498-43505 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T368 43594-43598 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T369 43623-43628 http://www.ebi.ac.uk/efo/EFO_0000825 denotes mouth
T370 43767-43768 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T371 43857-43864 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T372 44618-44625 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T373 44707-44708 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T374 44745-44746 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T375 44831-44832 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T376 45160-45167 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T377 45216-45218 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T378 45325-45326 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T379 45378-45381 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T380 45434-45435 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T381 45504-45505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T382 45779-45784 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T383 45845-45852 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T384 45929-45930 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T385 46017-46018 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T386 46207-46213 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T387 46381-46384 http://purl.obolibrary.org/obo/CLO_0008190 denotes Per
T388 46490-46495 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T389 46580-46584 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T390 46639-46645 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T391 46697-46701 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T392 46898-46903 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T393 47110-47111 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T394 47139-47143 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T395 47145-47146 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T396 47175-47179 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T397 47219-47220 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T398 47353-47355 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T399 47377-47381 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T400 47622-47624 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T401 47660-47664 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T402 47684-47685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T403 47886-47887 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T404 48280-48284 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T405 48353-48357 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T406 48361-48362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T407 48387-48388 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T408 48673-48674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T409 48757-48758 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T410 48784-48785 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T411 48840-48846 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T412 49194-49201 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T413 49213-49214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T414 49281-49282 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T415 49833-49834 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T416 49935-49936 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T417 50316-50317 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T418 50408-50409 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T419 50705-50709 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T420 50862-50863 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T421 51106-51107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T422 51353-51354 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T423 51480-51481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T424 51563-51564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T425 51704-51705 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T426 51774-51775 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T427 51871-51874 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T428 51978-51979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T429 52290-52291 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T430 52622-52623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T431 53096-53097 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 53214-53216 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T433 53544-53548 http://purl.obolibrary.org/obo/PR_000002979 denotes TAPS
T434 53612-53613 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T435 53661-53667 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T436 53759-53760 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T437 53855-53856 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T438 54415-54416 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T439 54796-54799 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T440 54796-54799 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T441 54966-54967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T442 54997-54998 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T443 55088-55090 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T444 55110-55112 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T445 55164-55166 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T446 55603-55608 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T447 55688-55690 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T448 55746-55751 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T449 55769-55770 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T450 55815-55816 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T451 55838-55839 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T452 55930-55931 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T453 56255-56256 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T454 56280-56281 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T455 56304-56308 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T456 56565-56568 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T457 56597-56598 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T458 56703-56708 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T459 56747-56748 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T460 56780-56785 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T461 56966-56967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T462 57314-57315 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T463 57906-57908 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T464 58174-58175 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T465 59025-59031 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T466 59072-59073 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T467 59175-59176 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T468 59460-59462 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T469 59995-60004 http://purl.obolibrary.org/obo/OBI_0000245 denotes organized
T470 60129-60135 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T471 60211-60217 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T472 60611-60614 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T473 61022-61023 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T474 61224-61225 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T475 61414-61415 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T476 61583-61586 http://purl.obolibrary.org/obo/CL_0000990 denotes DC1
T477 61614-61616 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T478 61644-61646 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T479 61644-61646 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T480 61812-61813 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T481 61919-61921 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T482 62153-62155 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T483 62218-62220 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T484 62218-62220 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T485 62265-62269 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T486 62337-62341 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T487 62406-62408 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T488 62485-62487 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T489 62533-62534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 3491-3499 Chemical denotes carriers http://purl.obolibrary.org/obo/CHEBI_78059
T2 4225-4233 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T3 4296-4304 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T4 4448-4464 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T5 4923-4926 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6 4959-4962 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T7 4995-5011 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T8 5161-5176 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T9 5177-5182 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T10 5198-5213 Chemical denotes fluorescent dye http://purl.obolibrary.org/obo/CHEBI_51121
T11 5210-5213 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T12 5533-5541 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T13 6080-6083 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T14 6190-6193 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T15 6194-6210 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T16 6270-6279 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T17 6381-6397 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T18 6459-6475 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T19 6484-6487 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T20 6519-6522 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T21 6613-6616 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T22 6667-6676 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T23 6745-6753 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T24 6828-6831 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T25 6933-6942 Chemical denotes indicator http://purl.obolibrary.org/obo/CHEBI_47867
T26 6950-6960 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T27 6950-6956 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T28 7373-7376 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T29 7610-7619 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T30 7756-7759 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T31 9650-9653 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T32 9834-9841 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T33 9851-9866 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T34 9873-9881 Chemical denotes aptamers http://purl.obolibrary.org/obo/CHEBI_140488
T35 9932-9942 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T36 10495-10510 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T37 10567-10576 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T38 10613-10621 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T39 11051-11060 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T40 11243-11252 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T41 11646-11653 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T42 11776-11785 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T43 12512-12522 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T44 12512-12518 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T45 12569-12572 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T46 13927-13937 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T47 13927-13933 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T48 14419-14425 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T49 14430-14433 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T50 15246-15255 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T51 15649-15658 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T52 16987-16989 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T53 19056-19058 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T54 19194-19196 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T55 20060-20067 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T56 20482-20484 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T57 21111-21114 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T58 21654-21657 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T59 23352-23354 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T60 23967-23969 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T61 25858-25866 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T62 25986-25992 Chemical denotes silica http://purl.obolibrary.org/obo/CHEBI_30563
T63 26583-26592 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T64 26739-26748 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T65 29615-29617 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T66 29753-29755 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T67 32819-32822 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T68 33761-33770 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T69 35303-35311 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T70 35360-35366 Chemical denotes silica http://purl.obolibrary.org/obo/CHEBI_30563
T71 36785-36800 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T72 37128-37131 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T73 37273-37278 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T74 37391-37399 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T75 37538-37546 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T76 37611-37619 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T77 37819-37822 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T78 38386-38398 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T79 38611-38623 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T80 38704-38716 Chemical denotes template RNA http://purl.obolibrary.org/obo/CHEBI_33699
T81 39548-39551 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T82 40499-40507 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T83 41967-41975 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T84 42098-42106 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T85 45512-45518 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T86 46167-46175 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T87 46312-46317 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T88 46447-46452 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T89 46586-46589 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T90 46703-46706 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T91 46793-46796 Chemical denotes cat http://purl.obolibrary.org/obo/CHEBI_32402
T92 47160-47169 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T93 47472-47480 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T94 47482-47487 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T95 47535-47550 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T96 47755-47758 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T97 47794-47810 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T98 48203-48208 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T99 48745-48753 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T100 49005-49013 Chemical denotes aluminum http://purl.obolibrary.org/obo/CHEBI_28984
T101 49025-49027 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T102 49264-49271 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T93821 49770-49775 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T20136 50183-50191 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T63187 50207-50210 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T68111 50956-50966 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T61897 50956-50962 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T63691 52731-52734 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T55476 52800-52802 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T75557 53000-53004 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T83003 53005-53008 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T99414 53259-53263 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T12523 53264-53267 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T47167 53403-53406 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6045 53475-53481 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T74345 53490-53494 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T27218 53495-53508 Chemical denotes hydroxymethyl http://purl.obolibrary.org/obo/CHEBI_24712
T25862 53509-53520 Chemical denotes methylamino http://purl.obolibrary.org/obo/CHEBI_44209
T6351 53537-53541 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T29057 53566-53571 Chemical denotes MgCl2 http://purl.obolibrary.org/obo/CHEBI_6636
T54464 53752-53755 Chemical denotes SDS http://purl.obolibrary.org/obo/CHEBI_8984
T50580 53802-53805 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T56525 54015-54020 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T73443 54225-54232 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T70592 54289-54293 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T8179 54294-54297 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T97460 54801-54808 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T41618 54809-54813 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T95865 54814-54821 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T15569 54822-54826 Chemical denotes EDTA http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755
T86686 55765-55767 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T89454 57609-57612 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T67772 61072-61074 Chemical denotes CC http://purl.obolibrary.org/obo/CHEBI_28940
T51063 61644-61646 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T87587 61756-61758 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T57515 61875-61877 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T44537 61919-61921 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T33478 62218-62220 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T13400 62290-62292 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T43387 62352-62354 Chemical denotes 5B http://purl.obolibrary.org/obo/CHEBI_27560
T55889 62362-62364 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T1291 62406-62408 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
1 63-73 Species denotes SARS-CoV-2 Tax:2697049
3 170-180 Species denotes SARS-CoV-2 Tax:2697049
5 270-280 Species denotes SARS-CoV-2 Tax:2697049
13 659-662 Gene denotes Dao Gene:1610
14 351-357 Species denotes people Tax:9606
15 381-391 Species denotes SARS-CoV-2 Tax:2697049
16 392-403 Species denotes coronavirus Tax:11118
17 953-963 Species denotes SARS-CoV-2 Tax:2697049
18 362-371 Disease denotes infection MESH:D007239
19 814-822 Disease denotes COVID-19 MESH:C000657245
31 2003-2004 Gene denotes N Gene:43740575
32 1286-1296 Species denotes SARS-CoV-2 Tax:2697049
33 1298-1345 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
34 1347-1358 Species denotes coronavirus Tax:11118
35 1946-1956 Species denotes SARS-CoV-2 Tax:2697049
36 2241-2251 Species denotes SARS-CoV-2 Tax:2697049
37 2372-2382 Species denotes SARS-CoV-2 Tax:2697049
38 1227-1251 Disease denotes coronavirus disease 2019 MESH:C000657245
39 1253-1261 Disease denotes COVID-19 MESH:C000657245
40 1430-1451 Disease denotes SARS-CoV-2 infections MESH:C000657245
41 2150-2158 Disease denotes COVID-19 MESH:C000657245
55 2955-2965 Species denotes SARS-CoV-2 Tax:2697049
56 2967-3014 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
57 3016-3027 Species denotes coronavirus Tax:11118
58 3096-3102 Species denotes people Tax:9606
59 3329-3335 Species denotes people Tax:9606
60 3463-3473 Species denotes SARS-CoV-2 Tax:2697049
61 3593-3601 Species denotes patients Tax:9606
62 2895-2919 Disease denotes coronavirus disease 2019 MESH:C000657245
63 2921-2929 Disease denotes COVID-19 MESH:C000657245
64 3205-3213 Disease denotes COVID-19 MESH:C000657245
65 3373-3393 Disease denotes SARS-CoV-2 infection MESH:C000657245
66 3449-3457 Disease denotes infected MESH:D007239
67 3540-3549 Disease denotes infection MESH:D007239
71 3847-3854 Species denotes persons Tax:9606
72 3838-3846 Disease denotes infected MESH:D007239
73 3882-3891 Disease denotes infection MESH:D007239
79 4249-4254 Species denotes human Tax:9606
80 4499-4509 Species denotes SARS-CoV-2 Tax:2697049
81 4285-4295 Species denotes SARS-CoV-2 Tax:2697049
82 4448-4464 Chemical denotes oligonucleotides MESH:D009841
83 4141-4161 Disease denotes SARS-CoV-2 infection MESH:C000657245
87 4556-4566 Species denotes SARS-CoV-2 Tax:2697049
88 4995-5011 Chemical denotes oligonucleotides MESH:D009841
89 5161-5176 Chemical denotes oligonucleotide MESH:D009841
92 5739-5749 Species denotes SARS-CoV-2 Tax:2697049
93 5502-5510 Disease denotes COVID-19 MESH:C000657245
98 6194-6210 Chemical denotes oligonucleotides MESH:D009841
99 6381-6397 Chemical denotes oligonucleotides MESH:D009841
100 6459-6475 Chemical denotes oligonucleotides MESH:D009841
101 6774-6803 Chemical denotes deoxynucleotide triphosphates
108 7053-7055 Gene denotes pH Gene:5053
109 6930-6932 Gene denotes pH Gene:5053
110 7290-7305 Species denotes influenza virus Tax:11309
111 7418-7428 Species denotes SARS-CoV-2 Tax:2697049
112 7655-7665 Species denotes SARS-CoV-2 Tax:2697049
113 6950-6960 Chemical denotes phenol red MESH:D010637
118 8622-8632 Species denotes SARS-CoV-2 Tax:2697049
119 8862-8872 Species denotes SARS-CoV-2 Tax:2697049
120 8485-8493 Disease denotes COVID-19 MESH:C000657245
121 8745-8753 Disease denotes COVID-19 MESH:C000657245
123 9529-9539 Species denotes SARS-CoV-2 Tax:2697049
135 10425-10452 Gene denotes open reading frame (ORF) 1a Gene:43740578
136 9694-9697 Gene denotes mix Gene:83881
137 9645-9648 Gene denotes Mix Gene:83881
138 10523-10524 Gene denotes N Gene:43740575
139 10391-10392 Gene denotes N Gene:43740575
140 10369-10370 Gene denotes N Gene:43740575
141 9563-9573 Species denotes SARS-CoV-2 Tax:2697049
142 10134-10144 Species denotes SARS-CoV-2 Tax:2697049
143 10346-10356 Species denotes SARS-CoV-2 Tax:2697049
144 9851-9866 Chemical denotes oligonucleotide MESH:D009841
145 10495-10510 Chemical denotes oligonucleotide MESH:D009841
151 11271-11272 Gene denotes N Gene:43740575
152 11260-11270 Species denotes SARS-CoV-2 Tax:2697049
153 11761-11771 Species denotes SARS-CoV-2 Tax:2697049
154 11414-11417 Chemical denotes ice MESH:D007053
155 11646-11653 Chemical denotes agarose MESH:D012685
158 12556-12558 Gene denotes pH Gene:5053
159 12512-12522 Chemical denotes phenol red MESH:D010637
164 13655-13656 Gene denotes N Gene:43740575
165 13673-13674 Gene denotes N Gene:43740575
166 13644-13654 Species denotes SARS-CoV-2 Tax:2697049
167 13927-13937 Chemical denotes phenol red MESH:D010637
170 14862-14869 Species denotes patient Tax:9606
171 14419-14425 Chemical denotes phenol MESH:D019800
173 15724-15725 Gene denotes N Gene:43740575
179 16699-16703 Gene denotes RdRp Gene:43740578
180 16485-16486 Gene denotes N Gene:43740575
181 16230-16231 Gene denotes N Gene:43740575
182 16097-16098 Gene denotes N Gene:43740575
183 16558-16568 Species denotes SARS-CoV-2 Tax:2697049
187 16799-16804 Gene denotes ORF1a Gene:43740578
188 16866-16867 Gene denotes N Gene:43740575
189 17045-17046 Gene denotes N Gene:43740575
191 17213-17223 Species denotes SARS-CoV-2 Tax:2697049
193 17601-17615 Gene denotes 3A and Table 1
195 17731-17741 Species denotes SARS-CoV-2 Tax:2697049
197 19000-19006 Disease denotes Wilson MESH:D006527
203 20164-20178 Gene denotes 3A and Table 1
204 19570-19580 Species denotes SARS-CoV-2 Tax:2697049
205 19865-19875 Species denotes SARS-CoV-2 Tax:2697049
206 20297-20303 Disease denotes Wilson MESH:D006527
207 20414-20420 Disease denotes Wilson MESH:D006527
209 22566-22576 Species denotes SARS-CoV-2 Tax:2697049
211 25986-25996 Chemical denotes silica gel MESH:D058428
217 26611-26612 Gene denotes N Gene:43740575
218 26600-26610 Species denotes SARS-CoV-2 Tax:2697049
219 27175-27185 Species denotes SARS-CoV-2 Tax:2697049
220 26641-26649 Disease denotes COVID-19 MESH:C000657245
221 27211-27219 Disease denotes infected MESH:D007239
223 30209-30211 Gene denotes pH Gene:5053
225 30534-30536 Gene denotes pH Gene:5053
228 32125-32127 Gene denotes pH Gene:5053
229 32264-32276 Chemical denotes Amies medium
232 32910-32911 Gene denotes N Gene:43740575
233 32687-32707 Disease denotes SARS-CoV-2 infection MESH:C000657245
238 33217-33222 Gene denotes ORF1a Gene:43740578
239 33167-33168 Gene denotes N Gene:43740575
240 33144-33145 Gene denotes N Gene:43740575
241 33367-33377 Species denotes SARS-CoV-2 Tax:2697049
245 34140-34141 Gene denotes N Gene:43740575
246 33923-33933 Species denotes SARS-CoV-2 Tax:2697049
247 34184-34204 Disease denotes SARS-CoV-2 infection MESH:C000657245
249 35360-35366 Chemical denotes silica MESH:D012822
252 36603-36613 Species denotes SARS-CoV-2 Tax:2697049
253 36785-36800 Chemical denotes oligonucleotide MESH:D009841
255 37273-37278 Chemical denotes water MESH:D014867
257 38133-38143 Species denotes SARS-CoV-2 Tax:2697049
261 38567-38569 Gene denotes pH Gene:5053
262 38492-38494 Gene denotes pH Gene:5053
263 38985-39001 Disease denotes reaction failure MESH:D006333
269 41261-41271 Species denotes SARS-CoV-2 Tax:2697049
270 41045-41065 Disease denotes SARS-CoV-2 infection MESH:C000657245
271 41347-41367 Disease denotes SARS-CoV-2 infection MESH:C000657245
272 41462-41470 Disease denotes COVID-19 MESH:C000657245
273 41651-41659 Disease denotes infected MESH:D007239
278 42986-42996 Species denotes SARS-CoV-2 Tax:2697049
279 43444-43451 Species denotes patient Tax:9606
280 43090-43098 Disease denotes COVID-19 MESH:C000657245
281 43204-43224 Disease denotes SARS-CoV-2 infection MESH:C000657245
285 43879-43889 Species denotes SARS-CoV-2 Tax:2697049
286 44155-44165 Species denotes SARS-CoV-2 Tax:2697049
287 44230-44240 Species denotes SARS-CoV-2 Tax:2697049
289 45012-45024 Chemical denotes Amies medium
296 46951-46954 Gene denotes mix Gene:83881
297 46412-46415 Gene denotes mix Gene:83881
298 46114-46124 Species denotes SARS-CoV-2 Tax:2697049
299 46574-46577 Species denotes CoV Tax:11118
300 46691-46694 Species denotes CoV Tax:11118
301 46447-46452 Chemical denotes water MESH:D014867
307 47365-47370 Gene denotes ORF1a Gene:43740578
308 47375-47376 Gene denotes N Gene:43740575
309 47569-47572 Gene denotes mix Gene:83881
310 47482-47487 Chemical denotes water MESH:D014867
311 47535-47550 Chemical denotes oligonucleotide MESH:D009841
314 47658-47659 Gene denotes N Gene:43740575
315 47716-47717 Gene denotes N Gene:43740575
323 48558-48561 Gene denotes mix Gene:83881
324 48473-48476 Gene denotes mix Gene:83881
325 48305-48308 Gene denotes mix Gene:83881
326 48167-48170 Gene denotes mix Gene:83881
327 48203-48208 Chemical denotes water MESH:D014867
328 49005-49013 Chemical denotes aluminum MESH:D000535
329 49264-49271 Chemical denotes agarose MESH:D012685
336 49636-49639 Gene denotes Mix Gene:83881
337 49899-49902 Gene denotes mix Gene:83881
338 49719-49722 Gene denotes mix Gene:83881
339 49770-49775 Chemical denotes water MESH:D014867
340 50207-50210 Chemical denotes CO2 MESH:D002245
341 50604-50609 Chemical denotes metal MESH:D008670
343 50801-50808 Gene denotes RT-LAMP
345 50956-50966 Chemical denotes phenol red MESH:D010637
352 52023-52026 Gene denotes mix Gene:83881
353 51464-51467 Gene denotes mix Gene:83881
354 51302-51309 Species denotes patient Tax:9606
355 51939-51946 Species denotes patient Tax:9606
356 51642-51647 Chemical denotes metal MESH:D008670
357 52488-52493 Chemical denotes metal MESH:D008670
372 53010-53012 Gene denotes pH Gene:5053
373 53112-53123 Species denotes Transposons Tax:2387
374 53000-53004 Chemical denotes tris
375 53005-53008 Chemical denotes HCl MESH:D006851
376 53752-53755 Chemical denotes SDS MESH:D012967
377 54015-54020 Chemical denotes water MESH:D014867
378 54225-54232 Chemical denotes ethanol MESH:D000431
379 54289-54297 Chemical denotes tris-HCl
380 54801-54808 Chemical denotes agarose MESH:D012685
381 54809-54821 Chemical denotes tris-acetate
382 54822-54826 Chemical denotes EDTA MESH:D004492
383 53544-53548 Disease denotes TAPS
384 53153-53157 Mutation denotes E54K p.E54K
385 53159-53164 Mutation denotes L372P p.L372P
388 55765-55776 Gene denotes S4, B and C Gene:6192
389 55490-55500 Species denotes SARS-CoV-2 Tax:2697049
392 56302-56303 Gene denotes N Gene:43740575
393 56291-56301 Species denotes SARS-CoV-2 Tax:2697049
395 57591-57594 Gene denotes S5B Gene:5711
397 58451-58457 Disease denotes Wilson MESH:D006527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 15-17 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T2 435-456 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T3 443-456 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T4 458-460 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T5 685-687 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T6 848-850 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T7 917-919 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T8 1056-1058 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T9 1176-1178 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T10 1533-1554 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T11 1541-1554 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T12 1595-1597 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T13 1692-1694 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T14 1735-1737 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T15 1759-1761 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T16 1909-1911 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T17 2025-2027 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T18 2213-2215 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T19 2278-2280 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T20 2340-2342 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T21 2395-2397 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T22 2528-2530 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T23 2692-2694 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T24 2858-2860 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T25 4822-4824 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T26 4862-4875 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T27 4862-4875 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T28 4877-4879 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T29 5650-5659 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T30 5709-5711 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T31 5935-5937 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T32 5946-5967 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T33 5954-5967 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T34 6008-6010 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T35 6024-6026 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T36 6060-6073 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T37 6060-6073 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T38 6107-6126 http://purl.obolibrary.org/obo/GO_0000732 denotes strand displacement
T39 6429-6442 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T40 6429-6442 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T41 6846-6848 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T42 7201-7203 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T43 7373-7390 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T44 7756-7773 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T45 8050-8052 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T46 8594-8596 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T47 8888-8890 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T48 8936-8938 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T49 9195-9197 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T50 9381-9383 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T51 9483-9485 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T52 9583-9585 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T53 9627-9629 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T54 9742-9755 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T55 9742-9755 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T56 10107-10109 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T57 10903-10905 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T58 11008-11010 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T59 11149-11151 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T60 11296-11298 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T61 11591-11593 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T62 11700-11702 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T63 11922-11924 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T64 11965-11967 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T65 12048-12050 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T66 12107-12109 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T67 12784-12786 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T68 12855-12857 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T69 13154-13156 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T70 13180-13182 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T71 13288-13290 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T72 13329-13331 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T73 13601-13603 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T74 14145-14147 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T75 14286-14288 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T76 14344-14346 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T77 14929-14931 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T78 15117-15119 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T79 15162-15164 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T80 15175-15177 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T81 15391-15393 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T82 15503-15505 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T83 15534-15536 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T84 15667-15669 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T85 15752-15754 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T86 15989-15991 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T87 16079-16081 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T88 16178-16180 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T89 16576-16578 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T90 16732-16734 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T91 16955-16957 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T92 17068-17070 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T93 17114-17116 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T94 17195-17197 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T95 17290-17292 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T96 17444-17446 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T97 17533-17541 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T98 17638-17640 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T99 17756-17758 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T100 17810-17812 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T101 17836-17838 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T102 18063-18065 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T103 18260-18262 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T104 18276-18278 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T105 18346-18348 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T106 18445-18447 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T107 18510-18512 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T108 18546-18548 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T109 18804-18806 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T110 19079-19081 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T111 19091-19093 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T112 19268-19270 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T113 19296-19298 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T114 19596-19598 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T115 19659-19661 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T116 19834-19836 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T117 20091-20093 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T118 20144-20146 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T119 20273-20275 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T120 20395-20397 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T121 20514-20516 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T122 20584-20586 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T123 20762-20764 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T124 20857-20859 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T125 20925-20927 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T126 21237-21239 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T127 21516-21518 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T128 21746-21748 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T129 21986-21988 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T130 22411-22413 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T131 22458-22460 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T132 22789-22791 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T133 22992-22994 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T134 23074-23076 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T135 23258-23260 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T136 24097-24099 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T137 24185-24187 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T138 24228-24230 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T139 24293-24295 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T140 24331-24333 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T141 24416-24418 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T142 24428-24430 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T143 24516-24518 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T144 24647-24649 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T145 24701-24703 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T146 24805-24807 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T147 24923-24925 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T148 25077-25079 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T149 25346-25348 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T150 25651-25653 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T151 25740-25742 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T152 25766-25768 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T153 26168-26170 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T154 26188-26190 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T155 26367-26369 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T156 26428-26430 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T157 27032-27034 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T158 27276-27278 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T159 27422-27424 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T160 27492-27494 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T161 27684-27686 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T162 27792-27794 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T163 27872-27874 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T164 28071-28073 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T165 28118-28120 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T166 28172-28174 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T167 28302-28304 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T168 28431-28433 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T169 28741-28743 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T170 28879-28881 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T171 29029-29031 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T172 29084-29086 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T173 29258-29260 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T174 29535-29537 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T175 29584-29586 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T176 29638-29640 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T177 29650-29652 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T178 29839-29841 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T179 29850-29852 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T180 29879-29881 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T181 30018-30020 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T182 30029-30031 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T183 30058-30060 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T184 30227-30229 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T185 30289-30291 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T186 30312-30314 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T187 30695-30697 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T188 30754-30756 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T189 31254-31256 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T190 31361-31363 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T191 31527-31529 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T192 31807-31809 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T193 32183-32185 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T194 32337-32339 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T195 32575-32577 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T196 32652-32654 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T197 32819-32836 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T198 32886-32888 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T199 32960-32962 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T200 33074-33076 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T201 33266-33268 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T202 33399-33401 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T203 33523-33525 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T204 33623-33625 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T205 33839-33841 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T206 34085-34087 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T207 34425-34427 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T208 34640-34642 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T209 34807-34809 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T210 34958-34960 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T211 35016-35018 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T212 35265-35275 http://purl.obolibrary.org/obo/GO_0004175 denotes proteinase
T213 35447-35449 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T214 35507-35509 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T215 35763-35765 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T216 35998-36000 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T217 36162-36164 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T218 36226-36228 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T219 37047-37049 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T220 37065-37067 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T221 37081-37083 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T222 37128-37145 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T223 37223-37225 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T224 37319-37321 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T225 37408-37410 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T226 37459-37461 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T227 37530-37532 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T228 37603-37605 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T229 37679-37681 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T230 37773-37775 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T231 37896-37898 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T232 37985-37987 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T233 38101-38103 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T234 38222-38224 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T235 38332-38334 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T236 38419-38421 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T237 38515-38517 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T238 38641-38654 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T239 38757-38759 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T240 39083-39085 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T241 39292-39294 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T242 39839-39841 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T243 40246-40248 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T244 40331-40333 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T245 40485-40487 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T246 40966-40968 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T247 41135-41137 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T248 41166-41168 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T249 41720-41722 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T250 41838-41840 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T251 41925-41927 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T252 42008-42010 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T253 42167-42169 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T254 42216-42218 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T255 42316-42318 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T256 42432-42434 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T257 42470-42472 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T258 42656-42658 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T259 42791-42793 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T260 43228-43230 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T261 43364-43375 http://purl.obolibrary.org/obo/GO_0065007 denotes regulations
T262 43782-43784 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T263 43849-43851 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T264 44100-44102 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T265 44431-44433 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T266 44563-44565 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T267 44610-44612 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T268 44807-44809 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T269 45244-45255 http://purl.obolibrary.org/obo/GO_0006810 denotes transported
T270 45506-45511 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T271 45539-45541 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T272 46076-46078 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T273 46850-46863 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T274 46850-46863 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T275 47082-47084 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T276 47188-47190 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T277 47231-47233 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T278 47278-47280 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T279 47421-47430 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T280 47586-47588 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T281 48272-48274 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T282 48290-48292 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T283 48465-48467 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T284 48871-48873 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T285 49108-49110 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T286 49303-49305 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T287 49442-49444 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T288 49618-49620 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T289 50223-50236 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T290 50801-50803 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T291 51000-51013 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T292 51245-51247 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T293 51286-51288 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T294 52214-52216 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T295 52588-52590 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T296 52731-52748 http://purl.obolibrary.org/obo/GO_0006309 denotes DNA fragmentation
T297 53378-53380 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T298 54352-54354 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T299 56401-56403 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T300 57039-57041 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T301 57627-57629 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T302 57681-57683 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T303 58039-58041 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T304 58087-58089 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T305 58143-58145 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T306 58248-58250 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T307 58307-58309 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T308 59688-59690 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T309 59841-59843 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T310 59963-59965 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T311 60284-60286 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T312 60407-60409 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T313 61142-61154 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T314 61666-61668 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T315 61700-61702 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T316 61778-61780 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T317 61834-61836 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T318 62017-62019 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T319 62091-62093 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T320 62257-62259 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T321 62329-62331 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 9282-9285 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T2 20989-20992 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T3 21962-21965 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T4 44833-44836 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T5 52668-52671 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T6 53149-53152 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T7 54373-54376 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-97 Sentence denotes A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples
T2 99-248 Sentence denotes A colorimetric isothermal RNA amplification method was shown to detect SARS-CoV-2 RNA in clinical samples with excellent sensitivity and specificity.
T3 250-294 Sentence denotes A colorful test for SARS-CoV-2 RNA detection
T4 295-404 Sentence denotes We need simple methods to rapidly test large numbers of people for infection with the SARS-CoV-2 coronavirus.
T5 405-541 Sentence denotes Quantitative PCR (qPCR) after reverse transcription (RT), the standard method, is very sensitive but requires expensive instrumentation.
T6 542-658 Sentence denotes Loop-mediated isothermal amplification (LAMP) is an alternative to qPCR that is faster and requires fewer resources.
T7 659-823 Sentence denotes Dao Thi et al. tested the RT-LAMP assay on several hundred clinical RNA samples isolated from pharyngeal swabs collected from individuals being tested for COVID-19.
T8 824-968 Sentence denotes They confirmed that the RT-LAMP assay was a simpler albeit less sensitive option compared to RT-qPCR for large-scale testing for SARS-CoV-2 RNA.
T9 969-1212 Sentence denotes These investigators also developed a simplified version of this method (direct swab–to–RT-LAMP assay) that did not require a prior RNA isolation step as well as a method for highly multiplexed sequencing of RT-LAMP reactions (LAMP-sequencing).
T10 1214-1222 Sentence denotes Abstract
T11 1223-1394 Sentence denotes The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge.
T12 1395-1492 Sentence denotes Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical.
T13 1493-1679 Sentence denotes Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods.
T14 1680-1880 Sentence denotes Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation.
T15 1881-2010 Sentence denotes Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene.
T16 2011-2159 Sentence denotes We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19.
T17 2160-2262 Sentence denotes We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA.
T18 2263-2499 Sentence denotes Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%.
T19 2500-2706 Sentence denotes We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay.
T20 2707-2876 Sentence denotes In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.
T21 2878-2890 Sentence denotes INTRODUCTION
T22 2891-3065 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 3066-3277 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 3278-3520 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 3521-3645 Sentence denotes This suggests that infection control strategies focusing on symptomatic patients are not sufficient to prevent virus spread.
T26 3646-3793 Sentence denotes Therefore, large-scale diagnostic methods are needed to determine the spread of the virus in populations quickly, comprehensively, and sensitively.
T27 3794-3892 Sentence denotes This would allow for the rapid isolation of infected persons during an existing wave of infection.
T28 3893-4130 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 4131-4263 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 4264-4465 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 4466-4551 Sentence denotes Therefore, an assay that detects SARS-CoV-2 RNA facilitates testing of large cohorts.
T32 4552-4830 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 4831-5047 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 5048-5214 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 5215-5466 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 5467-5660 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 5661-5785 Sentence denotes Therefore, increasing daily test capacities for RT-qPCR–based diagnostics for SARS-CoV-2 RNA detection is currently limited.
T38 5786-5916 Sentence denotes To accelerate and optimize such diagnostics, new scalable methods for RNA isolation and the detection of viral genomes are needed.
T39 5917-6023 Sentence denotes An alternative to RT-qPCR is reverse transcription loop-mediated isothermal amplification (RT-LAMP) (5–7).
T40 6024-6237 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 6238-6376 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 6377-6556 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 6557-6628 Sentence denotes These, in turn, serve as self-priming templates for the DNA polymerase.
T44 6629-6817 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 6818-6901 Sentence denotes To detect DNA production in RT-LAMP assays, various approaches have been described.
T46 6902-7016 Sentence denotes One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment.
T47 7017-7188 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 7189-7310 Sentence denotes Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9).
T49 7311-7433 Sentence denotes Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA.
T50 7434-7633 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 7634-7886 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 7887-8027 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 8028-8308 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 8309-8454 Sentence denotes For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used.
T55 8455-8907 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 8908-9046 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 9047-9209 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 9210-9446 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 9448-9455 Sentence denotes RESULTS
T60 9457-9552 Sentence denotes Establishing colorimetric RT-LAMP assay sensitivity using an artificial SARS-CoV-2 RNA template
T61 9553-9688 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 9689-9807 Sentence denotes This mix contains two enzymes, an engineered reverse transcriptase (RTx) and a strand-displacing polymerase (Bst 2.0).
T63 9808-10059 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 10060-10272 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 10273-10469 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 10470-10670 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 10671-10723 Sentence denotes The reaction was conducted for up to 1 hour at 65°C.
T68 10724-10815 Sentence denotes For time points > 30 to 35 min, the negative control frequently became yellowish (Fig. 1A).
T69 10816-10916 Sentence denotes This was caused by spurious amplification products, which is a well-known problem with RT-LAMP (14).
T70 10917-11121 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 11122-11188 Sentence denotes Fig. 1 Sensitivity of the RT-LAMP assay determined using IVT RNA.
T72 11189-11335 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 11336-11439 Sentence denotes At indicated times, samples were removed from the heating block and cooled on ice to stop the reaction.
T74 11440-11658 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 11659-11869 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 11871-11935 Sentence denotes Testing clinical RNA samples with the colorimetric RT-LAMP assay
T77 11936-12063 Sentence denotes To evaluate the colorimetric RT-LAMP assay, we needed to compare its sensitivity and specificity to a validated RT-qPCR method.
T78 12064-12188 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 12189-12320 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 12321-12597 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 12598-12849 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 12850-13110 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 13111-13211 Sentence denotes Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.
T84 13212-13324 Sentence denotes RNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate.
T85 13325-13554 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 13555-13797 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 13798-13965 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 13966-14024 Sentence denotes Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4.
T89 14025-14057 Sentence denotes Each line represents one sample.
T90 14058-14294 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 14295-14325 Sentence denotes Each dot is one sample (well).
T92 14326-14474 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 14475-14652 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 14653-14771 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 14772-15063 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 15064-15170 Sentence denotes This suggested a detection limit of the colorimetric RT-LAMP assay corresponding to a CT ≈ 30 for RT-qPCR.
T97 15171-15366 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 15367-15450 Sentence denotes The performance of each RT-qPCR run was validated using this as a positive control.
T99 15451-15691 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 15692-15868 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 15869-16163 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 16164-16311 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 16312-16460 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 16461-16584 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 16585-16723 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 16724-16991 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 16992-17162 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 17164-17237 Sentence denotes Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection
T109 17238-17346 Sentence denotes To determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples.
T110 17347-17422 Sentence denotes We assayed a total of 768 RNA samples obtained on different days (fig. S1).
T111 17423-17709 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 17710-17770 Sentence denotes Fig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.
T113 17771-17896 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 17897-18011 Sentence denotes The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated.
T115 18012-18127 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 18128-18183 Sentence denotes The 96-well plate shown in Fig. 2 is not included here.
T117 18184-18409 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 18410-18524 Sentence denotes The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay.
T119 18525-18818 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 18819-19060 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 19061-19175 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 19176-19267 Sentence denotes Fig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.
T123 19268-19275 Sentence denotes RT-LAMP
T124 19276-19295 Sentence denotes CT Pos Neg Sum
T125 19296-19327 Sentence denotes RT-qPCR Pos 0–25 51 0 51
T126 19328-19344 Sentence denotes 25–30 28 2 30
T127 19345-19361 Sentence denotes 30–35 4 16 20
T128 19362-19378 Sentence denotes 35–40 0 16 16
T129 19379-19401 Sentence denotes Neg Neg 2 649 651
T130 19402-19595 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 19596-19795 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 19796-19918 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 19919-20077 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 20078-20241 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 20242-20330 Sentence denotes The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval:
T136 20331-20447 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 20448-20486 Sentence denotes 91.4 to 99.3%) (Fig. 3B and table S2).
T138 20488-20539 Sentence denotes Multiplexed sequencing of RT-LAMP reaction products
T139 20540-20689 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 20690-20823 Sentence denotes Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences.
T141 20824-20960 Sentence denotes To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing).
T142 20961-21044 Sentence denotes LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding.
T143 21045-21166 Sentence denotes Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing.
T144 21167-21285 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 21286-21422 Sentence denotes After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters.
T146 21423-21534 Sentence denotes A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments.
T147 21535-21711 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 21712-21790 Sentence denotes Fig. 4 Multiplexed sequencing of RT-LAMP reaction products (LAMP-sequencing).
T149 21791-21833 Sentence denotes (A) Workflow for LAMP-sequencing is shown.
T150 21834-22012 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 22013-22129 Sentence denotes After tagmentation, each plate was pooled individually, followed by removal of excess adapters using size selection.
T152 22130-22475 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 22476-22507 Sentence denotes Each dot represents one sample.
T154 22508-22667 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 22668-22970 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 22971-23152 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 23153-23356 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 23357-23426 Sentence denotes This indicated that LAMP-sequencing amplified the targeted sequences.
T159 23427-23593 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 23594-23892 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 23893-23971 Sentence denotes For 754 of the 768 samples, we obtained enough reads to make a call (fig. S5).
T162 23972-24148 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 24149-24346 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 24347-24391 Sentence denotes Table 2 Summary of LAMP-sequencing results.
T165 24392-24646 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 24647-24654 Sentence denotes RT-LAMP
T167 24655-24674 Sentence denotes CT Pos Neg Sum
T168 24675-24732 Sentence denotes LAMP- sequencing Pos RT-qPCR Pos 0–25 49 0 49
T169 24733-24749 Sentence denotes 25–30 28 0 28
T170 24750-24764 Sentence denotes 30–35 4 0 4
T171 24765-24779 Sentence denotes 35–40 0 0 0
T172 24780-24798 Sentence denotes Neg Neg 0 0 0
T173 24799-24834 Sentence denotes Neg RT-qPCR Pos 0–25 0 0 0
T174 24835-24849 Sentence denotes 25–30 0 2 2
T175 24850-24866 Sentence denotes 30–35 0 16 16
T176 24867-24883 Sentence denotes 35–40 0 16 16
T177 24884-24906 Sentence denotes Neg Neg 2 637 639
T178 24907-24952 Sentence denotes Too few reads RT-qPCR Pos 0–25 2 0 2
T179 24953-24967 Sentence denotes 25–30 0 0 0
T180 24968-24982 Sentence denotes 30–35 0 0 0
T181 24983-24997 Sentence denotes 35–40 0 0 0
T182 24998-25018 Sentence denotes Neg Neg 0 12 12
T183 25019-25140 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 25141-25253 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 25254-25312 Sentence denotes LAMP-sequencing eliminated all of these samples (Fig. 4C).
T186 25313-25552 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 25553-25754 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 25756-25801 Sentence denotes A swab–to–RT-LAMP assay without RNA isolation
T189 25802-25917 Sentence denotes RNA isolation is time consuming, costly, and depends on reagents with potentially limited supply during a pandemic.
T190 25918-26131 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 26132-26350 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 26351-26543 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 26544-26676 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 26677-26873 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 26874-26903 Sentence denotes S6 and S7, and data file S1).
T196 26904-27232 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 27234-27289 Sentence denotes Testing clinical samples with the swab–to–RT-LAMP assay
T198 27290-27507 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 27508-27619 Sentence denotes As an additional precaution, we kept the samples in the cold (using an ice-cold metal block) whenever possible.
T200 27620-27727 Sentence denotes For testing large numbers of clinical samples, we performed the RT-LAMP assay using several 96-well plates.
T201 27728-27886 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 27887-28034 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 28035-28155 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 28156-28398 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 28399-28543 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 28544-28648 Sentence denotes We found that some positive samples did not induce a color change but did so when assayed a second time.
T207 28649-28724 Sentence denotes We therefore would recommend running this assay using technical duplicates.
T208 28725-28791 Sentence denotes Fig. 5 Swab–to–RT-LAMP assay of clinical pharyngeal swab samples.
T209 28792-28965 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 28966-29104 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 29105-29377 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 29378-29619 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 29620-29734 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 29735-29826 Sentence denotes Fig. 5A and table S3 show specificity and sensitivity values calculated from these numbers.
T215 29827-29857 Sentence denotes Hot swab–to–RT-LAMP RT-LAMP
T216 29858-29878 Sentence denotes CT Pos Neg Sum
T217 29879-29910 Sentence denotes RT-qPCR Pos 0–25 38 4 42
T218 29911-29927 Sentence denotes 25–30 17 5 22
T219 29928-29944 Sentence denotes 30–35 5 23 28
T220 29945-29961 Sentence denotes 35–40 0 36 36
T221 29962-29984 Sentence denotes Neg Neg 1 214 215
T222 29985-30002 Sentence denotes Sum 61 282 343
T223 30003-30036 Sentence denotes Direct swab–to–RT-LAMP RT-LAMP
T224 30037-30057 Sentence denotes CT Pos Neg Sum
T225 30058-30089 Sentence denotes RT-qPCR Pos 0–25 15 1 16
T226 30090-30106 Sentence denotes 25–30 6 11 17
T227 30107-30123 Sentence denotes 30–35 2 21 23
T228 30124-30140 Sentence denotes 35–40 3 23 26
T229 30141-30163 Sentence denotes Neg Neg 9 144 153
T230 30164-30181 Sentence denotes Sum 35 200 235
T231 30183-30240 Sentence denotes Heterogeneity of specimen pH in the swab–to–RT-LAMP assay
T232 30241-30451 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 30452-30558 Sentence denotes This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction.
T234 30559-30645 Sentence denotes This might have affected the interpretability of the measurement at 30 min (ΔOD30min).
T235 30646-30709 Sentence denotes We investigated how this pH shift influenced the RT-LAMP assay.
T236 30710-30842 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 30843-31025 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 31026-31208 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 31209-31278 Sentence denotes Fig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.
T240 31279-31403 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 31404-31541 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 31542-31602 Sentence denotes Also, the 40-min time point was not available for one plate.
T243 31603-31728 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 31729-32030 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 32031-32104 Sentence denotes The latter shows better separation between positive and negative samples.
T246 32105-32250 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 32251-32416 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 32417-32589 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 32591-32601 Sentence denotes DISCUSSION
T250 32602-32708 Sentence denotes Here, we evaluated the use and suitability of the RT-LAMP assay for the detection of SARS-CoV-2 infection.
T251 32709-32847 Sentence denotes We also developed LAMP-sequencing as a fully scalable alternative to colorimetric or fluorometric analysis of DNA amplification reactions.
T252 32848-33059 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 33060-33223 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 33224-33492 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 33493-33561 Sentence denotes For samples with CT > 30, the RT-LAMP assay was much less sensitive.
T256 33562-33679 Sentence denotes However, there is debate about which CT value for a positive RT-qPCR result should be considered clinically relevant.
T257 33680-33778 Sentence denotes Vogels et al. (16) indicate that a CT value above 36 corresponds to less than 10 molecules of RNA.
T258 33779-33945 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 33946-34205 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 34206-34467 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 34468-34558 Sentence denotes Furthermore, alternative sample types, e.g., sputum or stool (29), might be more reliable.
T262 34559-34785 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 34786-34901 Sentence denotes Compatibility of the RT-LAMP assay with direct saliva specimens has been shown using spike-in experiments (22, 34).
T264 34902-35049 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 35050-35312 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 35313-35530 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 35531-35786 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 35787-35932 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 35933-36130 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 36131-36310 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 36311-36515 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 36516-36545 Sentence denotes S6 and S7, and data file S1).
T273 36546-36721 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 36722-36906 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 36907-37004 Sentence denotes However, these applications have yet to be tested with large numbers of diverse clinical samples.
T276 37005-37073 Sentence denotes There are several differences between the RT-LAMP assay and RT-qPCR.
T277 37074-37303 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 37304-37378 Sentence denotes This makes the RT-LAMP assay more amenable for point-of-care applications.
T279 37379-37496 Sentence denotes Second, the reagents for the RT-LAMP assay are different from the ones used for RT-qPCR and are supplier independent.
T280 37497-37667 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 37668-37842 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 37843-37980 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 37981-38084 Sentence denotes The RT-LAMP assay overcomes this problem and therefore will be a more scalable method for mass testing.
T284 38086-38151 Sentence denotes Application of RT-LAMP and LAMP-sequencing for SARS-CoV-2 testing
T285 38152-38259 Sentence denotes With its good sensitivity for samples up to CT ≈ 30, the colorimetric RT-LAMP assay has several advantages:
T286 38260-38331 Sentence denotes It is fast, inexpensive, and it can be evaluated without any equipment.
T287 38332-38580 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 38581-38745 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 38746-39023 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 39024-39097 Sentence denotes It would be desirable to have a similar precaution for the RT-LAMP assay.
T291 39098-39226 Sentence denotes A multiplexed fluorescence readout might provide this (34) but comes at the expense of the simplicity of a colorimetric readout.
T292 39227-39521 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 39522-39708 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 39709-39853 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 39854-40089 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 40090-40197 Sentence denotes Thus, LAMP-sequencing could become an important part of workflows for routine testing of large populations.
T297 40198-40409 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 40410-40635 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 40636-40679 Sentence denotes There are several limitations to our study.
T300 40680-40790 Sentence denotes We used surplus RNA sample material from a diagnostic laboratory rather than newly collected clinical samples.
T301 40791-40894 Sentence denotes The criteria for testing individuals may have influenced cohort characteristics and hence our findings.
T302 40895-41066 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 41067-41278 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 41279-41479 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 41480-41679 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 41680-41782 Sentence denotes We used LAMP-sequencing to validate the RT-LAMP assay results and did not use it as a diagnostic tool.
T307 41783-41960 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 41961-42082 Sentence denotes Also, reagents such as the primer sets for the RT-LAMP assay may be subject to production-dependent quality fluctuations.
T309 42083-42196 Sentence denotes Therefore, all reagents must be precisely validated (batch control) before using an RT-LAMP assay diagnostically.
T310 42197-42311 Sentence denotes Application of the RT-LAMP assay has great potential, even more so as more sensitive primer sets become available.
T311 42312-42452 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 42453-42651 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 42652-42876 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 42878-42899 Sentence denotes MATERIALS AND METHODS
T315 42901-42913 Sentence denotes Study design
T316 42914-43099 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 43100-43311 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 43312-43518 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 43519-43693 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 43694-43947 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 43948-44023 Sentence denotes This study was conducted in Heidelberg, Germany in March and April of 2020.
T322 44024-44302 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 44303-44577 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 44578-44727 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 44728-44907 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 44909-44933 Sentence denotes Clinical sample handling
T327 44934-45047 Sentence denotes Specimens were collected as nasopharyngeal and oropharyngeal flocked swabs in Amies medium (eSwab, Copan Italia).
T328 45048-45220 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 45221-45407 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 45408-45519 Sentence denotes Samples were processed in a biosafety level 2 cabinet until inactivation by heat or mixing with a lysis buffer.
T331 45521-45546 Sentence denotes RNA isolation and RT-qPCR
T332 45547-45894 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 45895-46075 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 46076-46223 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 46224-46380 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 46381-46594 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 46595-46711 Sentence denotes 53-0776-96; TIB MOLBIOL Syntheselabor GmbH, Berlin, Germany) or LightMix Modular SARS and Wuhan CoV N gene (cat. no.
T338 46712-46801 Sentence denotes 53-0775-96; TIB MOLBIOL), 0.5 μl of LightMix Modular EAV RNA Extraction Control (cat. no.
T339 46802-46939 Sentence denotes 66-0909-96; TIB MOLBIOL), and 0.1 μl of reverse transcriptase enzyme (LightCycler Multiplex RNA Virus Master, Roche, Basel, Switzerland).
T340 46940-47058 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 47059-47144 Sentence denotes The performance of the RT-qPCR was validated using a positive control for the E gene.
T342 47145-47229 Sentence denotes A total of 103 molecules of E gene RNA per RT-qPCR reaction correspond to a CT ≈ 30.
T343 47231-47273 Sentence denotes RT-LAMP primer design and positive control
T344 47274-47489 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 47490-47625 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 47626-47999 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 48001-48084 Sentence denotes Liquid handling using 96-well plates and precautions taken to prevent contamination
T348 48085-48151 Sentence denotes To prevent cross-contamination, we have taken several precautions.
T349 48152-48258 Sentence denotes The 10× primer mix was prepared with nuclease-free water (AM9937, Ambion) and stored in aliquots at −20°C.
T350 48259-48427 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 48428-48548 Sentence denotes The 96-well PCR plate containing the RT-LAMP mix was covered with an Society for Biomolecular Screening (SBS) plate lid.
T352 48549-48694 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 48695-48866 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 48867-49086 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 49087-49301 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 49303-49316 Sentence denotes RT-LAMP assay
T357 49317-49458 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 49459-49793 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 49794-49828 Sentence denotes Values given are for one reaction:
T360 49829-50108 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 50109-50290 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 50291-50474 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 50475-50625 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 50626-50676 Sentence denotes This intensifies the color before the measurement.
T365 50677-50777 Sentence denotes Photographs were taken with cell phone cameras or the scanner function of an office copying machine.
T366 50779-50817 Sentence denotes Quantification of the RT-LAMP reaction
T367 50818-50934 Sentence denotes Absorbance measurements were performed with a Spark Cyto or Infinite M200 (Tecan) at 434 and 560 nm with 25 flashes.
T368 50935-51095 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 51096-51202 Sentence denotes To obtain a good readout of the color change, absorbance at 560 nm was substracted from the one at 434 nm.
T370 51203-51235 Sentence denotes This difference was denoted ΔOD.
T371 51237-51258 Sentence denotes Swab–to–RT-LAMP assay
T372 51259-51374 Sentence denotes For direct and hot swab–to–RT-LAMP assays, patient swab specimens were transferred first onto a 96-well seed plate.
T373 51375-51535 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 51536-51654 Sentence denotes The plate was sealed using a transparent adhesive foil (GK480-OS, Kisker Biotech) and kept on an ice-cold metal block.
T375 51655-51836 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 51837-51902 Sentence denotes The seed plate was cooled down to 4°C on an ice-cold metal block.
T377 51903-52036 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 52037-52122 Sentence denotes This plate was also sealed with transparent adhesive foil (GK480-OS, Kisker Biotech).
T379 52123-52196 Sentence denotes Both plates were then incubated at 65°C for the LAMP reaction to proceed.
T380 52197-52358 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 52359-52509 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 52511-52533 Sentence denotes LAMP-sequencing method
T383 52534-52754 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 52755-52803 Sentence denotes The relevant primers are summarized in table S4.
T385 52804-53111 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 53112-53324 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 53325-53669 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 53670-53718 Sentence denotes The reactions were incubated at 55°C for 10 min.
T389 53719-53791 Sentence denotes Reactions were stopped by adding SDS to a final concentration of 0.033%.
T390 53792-53958 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 53959-54075 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 54076-54305 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 54306-54700 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 54701-54872 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 54873-55213 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 55214-55327 Sentence denotes For trimming of the reads (i.e., removal of P7 Illumina adapter sequences), cutadapt (version 2.8) (42) was used.
T397 55328-55464 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 55465-55602 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 55603-55692 Sentence denotes Virus genome coverage was determined with the samtools depth command (version 1.10) (45).
T400 55693-55778 Sentence denotes Using bwa-mem, 80.6% of reads could be mapped to the virus genome (fig. S4, B and C).
T401 55779-55868 Sentence denotes To analyze the remaining sequences, a k-mer analysis using a custom script was performed.
T402 55869-56044 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 56045-56141 Sentence denotes This is explained by the fact that LAMP products can consist of complex sequence rearrangements.
T404 56142-56254 Sentence denotes For classification of samples by LAMP-sequencing, reads were assigned to wells and counted using custom scripts.
T405 56255-56478 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 56479-56596 Sentence denotes Sequencing reads were grouped by UMI and by position of the matched sequence with the aim of removing PCR duplicates.
T407 56597-56737 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 56738-56850 Sentence denotes There is a very wide gap in the number of virus-matching reads between positive and negative samples (fig. S5A):
T409 56851-56908 Sentence denotes The count is either below 7000 UMIs or above 45,000 UMIs.
T410 56909-57019 Sentence denotes This is why we placed the decision threshold for scoring a sample as LAMP-sequencing positive within this gap.
T411 57020-57309 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 57310-57456 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 57457-57635 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 57636-57780 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 57782-57802 Sentence denotes Statistical analysis
T416 57803-57940 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 57941-58019 Sentence denotes Sensitivity and specificity values were obtained from count tables as follows:
T418 58020-58157 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 58158-58321 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 58322-58544 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 58545-58709 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.
T422 58711-58726 Sentence denotes Acknowledgments
T423 58727-58738 Sentence denotes We thank V.
T424 58739-58752 Sentence denotes Pelechano, X.
T425 58753-58764 Sentence denotes Yin, and V.
T426 58765-58826 Sentence denotes Lohmann for helpful discussions and sharing unpublished work.
T427 58827-58838 Sentence denotes We thank U.
T428 58839-59045 Sentence denotes Merle for providing specimens and the diagnostic laboratory team at Heidelberg University Hospital for providing RNA samples isolated from pharyngeal swabs collected from patients being tested for COVID-19.
T429 59046-59057 Sentence denotes We thank V.
T430 59058-59077 Sentence denotes Sonntag-Buck, A.-M.
T431 59078-59088 Sentence denotes Heuser, I.
T432 59089-59099 Sentence denotes Ambiel, S.
T433 59100-59110 Sentence denotes Winter, T.
T434 59111-59125 Sentence denotes Müller, and S.
T435 59126-59165 Sentence denotes Horner for excellent technical support.
T436 59166-59177 Sentence denotes We thank A.
T437 59178-59195 Sentence denotes Uvarovskii and S.
T438 59196-59235 Sentence denotes Ovchinnikova for IT-related help and S.
T439 59236-59249 Sentence denotes Kreger and U.
T440 59250-59286 Sentence denotes Jäkle for additional technical help.
T441 59287-59379 Sentence denotes Funding: V.L.D.T., A.F., and P.C. were supported by the Chica and Heinz Schaller foundation.
T442 59380-59453 Sentence denotes M.K. was supported by the Deutsche Forschungsgemeinschaft (DFG; grant no.
T443 59454-59466 Sentence denotes KN498/11-1).
T444 59467-59523 Sentence denotes S.B. was supported by the Heisenberg program of the DFG.
T445 59524-59612 Sentence denotes Author contributions: V.L.D.T., H.-G.K., M.K., and S.A. conceived and planned the study.
T446 59613-59773 Sentence denotes V.L.D.T., M.M., K.B., and M.K. planned and designed the experiments on the RT-LAMP assay and performed them together with Daniel Kirrmaier, A.F., S.K., and P.C.
T447 59774-59855 Sentence denotes V.L.D.T., K.B., and M.K. performed the experiments for the swab–to–RT-LAMP assay.
T448 59856-59943 Sentence denotes K.H. designed the LAMP-sequencing assay and performed it with Daniel Kirrmaier and M.K.
T449 59944-60114 Sentence denotes K.B. performed the RT-qPCR analyses of samples and organized, together with I.B.M., P.S., Dina Khalid, and H.-G.K., provision of the samples by the diagnostic laboratory.
T450 60115-60177 Sentence denotes D.P. and C.G. tested sample handling and logistics strategies.
T451 60178-60247 Sentence denotes V.L.D.T., M.K., M.L.S., and S.B. tested viral inactivation protocols.
T452 60248-60336 Sentence denotes S.A. performed data analysis of the RT-LAMP experiments, together with L.P.M.K. and K.H.
T453 60337-60376 Sentence denotes K.H. analyzed the LAMP-sequencing data.
T454 60377-60420 Sentence denotes V.L.D.T. analyzed the swab–to–RT-LAMP data.
T455 60421-60502 Sentence denotes V.L.D.T., K.H., P.C., L.P.M.K., M.K., and S.A. analyzed and interpreted the data.
T456 60503-60584 Sentence denotes V.L.D.T., K.H., M.K., and S.A. wrote the manuscript, with input from all authors.
T457 60585-60637 Sentence denotes Competing interests: P.S. has consulted for Janssen.
T458 60638-60702 Sentence denotes The other authors declare that they have no competing interests.
T459 60703-60735 Sentence denotes Data and materials availability:
T460 60736-60824 Sentence denotes All data associated with this study are in the main text or the Supplementary Materials.
T461 60825-60993 Sentence denotes The R code used to perform analyses and produce figures can be found on GitHub, together with all raw data tables: https://github.com/anders-biostat/LAMP-Paper-Figures.
T462 60994-61215 Sentence denotes This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
T463 61216-61298 Sentence denotes To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
T464 61299-61500 Sentence denotes This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using this material.
T465 61502-61525 Sentence denotes SUPPLEMENTARY MATERIALS
T466 61526-61586 Sentence denotes stm.sciencemag.org/cgi/content/full/scitranslmed.abc7075/DC1
T467 61587-61608 Sentence denotes Materials and Methods
T468 61609-61617 Sentence denotes Fig. S1.
T469 61618-61638 Sentence denotes Design of the study.
T470 61639-61647 Sentence denotes Fig. S2.
T471 61648-61750 Sentence denotes Comparison of the RT-LAMP assay with CT values from RT-qPCR using primer sets E-Sarbeco and N-Sarbeco.
T472 61751-61759 Sentence denotes Fig. S3.
T473 61760-61869 Sentence denotes Comparison of the RT-LAMP assay using primer set 1a-A with CT values from RT-qPCR using primer set E-Sarbeco.
T474 61870-61878 Sentence denotes Fig. S4.
T475 61879-61913 Sentence denotes Analysis of LAMP-sequencing reads.
T476 61914-61922 Sentence denotes Fig. S5.
T477 61923-61966 Sentence denotes Sample classification with LAMP-sequencing.
T478 61967-61975 Sentence denotes Fig. S6.
T479 61976-62073 Sentence denotes RNA stability and detection limit of the RT-LAMP assay in pharyngeal swab specimens with IVT RNA.
T480 62074-62082 Sentence denotes Fig. S7.
T481 62083-62146 Sentence denotes Swab–to–RT-LAMP assay titration of positive COVID-19 specimens.
T482 62147-62156 Sentence denotes Table S1.
T483 62157-62211 Sentence denotes Sequences of primers and amplicons used in this study.
T484 62212-62221 Sentence denotes Table S2.
T485 62222-62283 Sentence denotes Sensitivity and specificity of the RT-LAMP test from Fig. 3B.
T486 62284-62293 Sentence denotes Table S3.
T487 62294-62355 Sentence denotes Sensitivity and specificity of the RT-LAMP test from Fig. 5B.
T488 62356-62365 Sentence denotes Table S4.
T489 62366-62399 Sentence denotes Primers used for LAMP-sequencing.
T490 62400-62409 Sentence denotes Table S5.
T491 62410-62474 Sentence denotes Overview of time requirements for various sample handling steps.
T492 62475-62488 Sentence denotes Data File S1.
T493 62489-62507 Sentence denotes Raw data for figs.
T494 62508-62518 Sentence denotes S6 and S7.
T495 62520-62577 Sentence denotes View/request a protocol for this paper from Bio-protocol.