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PMC:7574920 / 32591-42876 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T126 228-231 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T127 578-582 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T128 787-790 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T129 828-831 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T130 1183-1186 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T131 1368-1372 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T132 1868-1875 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T133 1922-1928 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T134 1932-1937 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T135 2069-2075 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T136 2242-2248 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T137 2454-2457 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T138 2712-2720 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 2841-2844 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T140 3078-3081 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T141 3337-3340 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T142 3475-3478 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T143 3759-3762 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T144 3877-3880 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T145 4537-4540 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T146 5228-5231 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T147 6122-6125 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T148 6240-6243 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T149 6327-6331 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T150 8105-8108 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T151 8994-9001 Body_part denotes pharynx http://purl.org/sig/ont/fma/fma46688
T152 9365-9368 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T153 10045-10051 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 1368-1372 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T4 1922-1928 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 1932-1937 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T6 2069-2075 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T7 2242-2248 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T8 6427-6431 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T9 7310-7315 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T10 7801-7806 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T11 8994-9001 Body_part denotes pharynx http://purl.obolibrary.org/obo/UBERON_0006562
T12 10045-10051 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T77 96-104 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 107-116 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 776-784 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 1332-1340 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 1593-1601 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 1604-1613 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 4012-4020 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 5542-5550 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 8454-8462 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 8465-8474 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 8630-8640 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T88 8670-8678 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T89 8756-8764 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 8767-8776 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 8871-8879 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T280 155-156 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T281 321-322 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T282 422-423 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T283 435-442 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T284 472-478 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T285 530-532 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T286 555-556 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T287 578-582 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T288 609-610 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T289 650-651 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T290 1021-1022 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T291 1122-1123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T292 1139-1141 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T293 1313-1314 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T294 1389-1390 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T295 1551-1552 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T296 1591-1592 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T297 1615-1616 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T298 1683-1689 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T299 1695-1697 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T300 2259-2262 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T301 2302-2304 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T302 2306-2308 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T303 2569-2571 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T304 2738-2740 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T305 2970-2971 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T306 3397-3398 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T307 3415-3419 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T308 3591-3592 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T309 3656-3657 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T310 3950-3952 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T311 4034-4038 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T312 4084-4085 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T313 4258-4260 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T314 4265-4266 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T315 4297-4299 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T316 4359-4365 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T317 4507-4508 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T318 4587-4597 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T319 4673-4674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T320 4696-4697 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T321 5357-5358 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T322 5453-5454 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T323 5485-5492 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T324 5553-5560 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T325 5645-5648 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T326 5846-5849 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T327 6111-6112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T328 6174-6179 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T329 6196-6197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 6327-6331 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T331 6384-6385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 6418-6419 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T333 6427-6431 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T334 6463-6464 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T335 6507-6508 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T336 6562-6564 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T337 6612-6613 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T338 7166-7167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T339 7577-7584 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T340 7790-7791 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T341 7810-7817 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T342 8130-8131 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 8217-8224 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T344 8452-8453 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 8681-8686 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T346 8754-8755 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T347 8803-8804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T348 8937-8938 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T349 8966-8967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T350 8994-9001 http://purl.obolibrary.org/obo/UBERON_0001042 denotes pharynx
T351 8994-9001 http://purl.obolibrary.org/obo/UBERON_0006562 denotes pharynx
T352 9173-9174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T353 9317-9318 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 9639-9642 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T355 9780-9787 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T356 9855-9860 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T357 9919-9926 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T358 9930-9931 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T359 9963-9970 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T360 10129-10133 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T361 10168-10173 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T362 10185-10190 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T363 10218-10219 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 10273-10277 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T67 228-231 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T68 1170-1179 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T69 2712-2720 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T70 2769-2775 Chemical denotes silica http://purl.obolibrary.org/obo/CHEBI_30563
T71 4194-4209 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T72 4537-4540 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T73 4682-4687 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T74 4800-4808 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T75 4947-4955 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T76 5020-5028 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T77 5228-5231 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T78 5795-5807 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T79 6020-6032 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T80 6113-6125 Chemical denotes template RNA http://purl.obolibrary.org/obo/CHEBI_33699
T81 6957-6960 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T82 7908-7916 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T83 9376-9384 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T84 9507-9515 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
232 319-320 Gene denotes N Gene:43740575
233 96-116 Disease denotes SARS-CoV-2 infection MESH:C000657245
238 626-631 Gene denotes ORF1a Gene:43740578
239 576-577 Gene denotes N Gene:43740575
240 553-554 Gene denotes N Gene:43740575
241 776-786 Species denotes SARS-CoV-2 Tax:2697049
245 1549-1550 Gene denotes N Gene:43740575
246 1332-1342 Species denotes SARS-CoV-2 Tax:2697049
247 1593-1613 Disease denotes SARS-CoV-2 infection MESH:C000657245
249 2769-2775 Chemical denotes silica MESH:D012822
252 4012-4022 Species denotes SARS-CoV-2 Tax:2697049
253 4194-4209 Chemical denotes oligonucleotide MESH:D009841
255 4682-4687 Chemical denotes water MESH:D014867
257 5542-5552 Species denotes SARS-CoV-2 Tax:2697049
261 5976-5978 Gene denotes pH Gene:5053
262 5901-5903 Gene denotes pH Gene:5053
263 6394-6410 Disease denotes reaction failure MESH:D006333
269 8670-8680 Species denotes SARS-CoV-2 Tax:2697049
270 8454-8474 Disease denotes SARS-CoV-2 infection MESH:C000657245
271 8756-8776 Disease denotes SARS-CoV-2 infection MESH:C000657245
272 8871-8879 Disease denotes COVID-19 MESH:C000657245
273 9060-9068 Disease denotes infected MESH:D007239

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T196 61-63 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T197 228-245 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T198 295-297 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T199 369-371 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T200 483-485 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T201 675-677 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T202 808-810 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T203 932-934 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T204 1032-1034 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T205 1248-1250 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T206 1494-1496 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T207 1834-1836 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T208 2049-2051 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T209 2216-2218 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T210 2367-2369 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T211 2425-2427 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T212 2674-2684 http://purl.obolibrary.org/obo/GO_0004175 denotes proteinase
T213 2856-2858 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T214 2916-2918 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T215 3172-3174 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T216 3407-3409 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T217 3571-3573 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T218 3635-3637 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T219 4456-4458 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T220 4474-4476 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T221 4490-4492 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T222 4537-4554 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T223 4632-4634 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T224 4728-4730 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T225 4817-4819 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T226 4868-4870 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T227 4939-4941 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T228 5012-5014 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T229 5088-5090 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T230 5182-5184 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T231 5305-5307 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T232 5394-5396 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T233 5510-5512 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T234 5631-5633 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T235 5741-5743 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T236 5828-5830 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T237 5924-5926 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T238 6050-6063 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T239 6166-6168 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T240 6492-6494 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T241 6701-6703 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T242 7248-7250 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T243 7655-7657 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T244 7740-7742 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T245 7894-7896 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T246 8375-8377 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T247 8544-8546 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T248 8575-8577 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T249 9129-9131 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T250 9247-9249 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T251 9334-9336 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T252 9417-9419 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T253 9576-9578 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T254 9625-9627 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T255 9725-9727 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T256 9841-9843 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T257 9879-9881 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T258 10065-10067 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T259 10200-10202 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T249 0-10 Sentence denotes DISCUSSION
T250 11-117 Sentence denotes Here, we evaluated the use and suitability of the RT-LAMP assay for the detection of SARS-CoV-2 infection.
T251 118-256 Sentence denotes We also developed LAMP-sequencing as a fully scalable alternative to colorimetric or fluorometric analysis of DNA amplification reactions.
T252 257-468 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 469-632 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 633-901 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 902-970 Sentence denotes For samples with CT > 30, the RT-LAMP assay was much less sensitive.
T256 971-1088 Sentence denotes However, there is debate about which CT value for a positive RT-qPCR result should be considered clinically relevant.
T257 1089-1187 Sentence denotes Vogels et al. (16) indicate that a CT value above 36 corresponds to less than 10 molecules of RNA.
T258 1188-1354 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 1355-1614 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 1615-1876 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 1877-1967 Sentence denotes Furthermore, alternative sample types, e.g., sputum or stool (29), might be more reliable.
T262 1968-2194 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 2195-2310 Sentence denotes Compatibility of the RT-LAMP assay with direct saliva specimens has been shown using spike-in experiments (22, 34).
T264 2311-2458 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 2459-2721 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 2722-2939 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 2940-3195 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 3196-3341 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 3342-3539 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 3540-3719 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 3720-3924 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 3925-3954 Sentence denotes S6 and S7, and data file S1).
T273 3955-4130 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 4131-4315 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 4316-4413 Sentence denotes However, these applications have yet to be tested with large numbers of diverse clinical samples.
T276 4414-4482 Sentence denotes There are several differences between the RT-LAMP assay and RT-qPCR.
T277 4483-4712 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 4713-4787 Sentence denotes This makes the RT-LAMP assay more amenable for point-of-care applications.
T279 4788-4905 Sentence denotes Second, the reagents for the RT-LAMP assay are different from the ones used for RT-qPCR and are supplier independent.
T280 4906-5076 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 5077-5251 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 5252-5389 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 5390-5493 Sentence denotes The RT-LAMP assay overcomes this problem and therefore will be a more scalable method for mass testing.
T284 5495-5560 Sentence denotes Application of RT-LAMP and LAMP-sequencing for SARS-CoV-2 testing
T285 5561-5668 Sentence denotes With its good sensitivity for samples up to CT ≈ 30, the colorimetric RT-LAMP assay has several advantages:
T286 5669-5740 Sentence denotes It is fast, inexpensive, and it can be evaluated without any equipment.
T287 5741-5989 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 5990-6154 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 6155-6432 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 6433-6506 Sentence denotes It would be desirable to have a similar precaution for the RT-LAMP assay.
T291 6507-6635 Sentence denotes A multiplexed fluorescence readout might provide this (34) but comes at the expense of the simplicity of a colorimetric readout.
T292 6636-6930 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 6931-7117 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 7118-7262 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 7263-7498 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 7499-7606 Sentence denotes Thus, LAMP-sequencing could become an important part of workflows for routine testing of large populations.
T297 7607-7818 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 7819-8044 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 8045-8088 Sentence denotes There are several limitations to our study.
T300 8089-8199 Sentence denotes We used surplus RNA sample material from a diagnostic laboratory rather than newly collected clinical samples.
T301 8200-8303 Sentence denotes The criteria for testing individuals may have influenced cohort characteristics and hence our findings.
T302 8304-8475 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 8476-8687 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 8688-8888 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 8889-9088 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 9089-9191 Sentence denotes We used LAMP-sequencing to validate the RT-LAMP assay results and did not use it as a diagnostic tool.
T307 9192-9369 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 9370-9491 Sentence denotes Also, reagents such as the primer sets for the RT-LAMP assay may be subject to production-dependent quality fluctuations.
T309 9492-9605 Sentence denotes Therefore, all reagents must be precisely validated (batch control) before using an RT-LAMP assay diagnostically.
T310 9606-9720 Sentence denotes Application of the RT-LAMP assay has great potential, even more so as more sensitive primer sets become available.
T311 9721-9861 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 9862-10060 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 10061-10285 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.