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PMC:7574920 / 38086-42876 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T147 627-630 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T148 745-748 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T149 832-836 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T150 2610-2613 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T151 3499-3506 Body_part denotes pharynx http://purl.org/sig/ont/fma/fma46688
T152 3870-3873 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T153 4550-4556 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 932-936 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T9 1815-1820 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T10 2306-2311 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T11 3499-3506 Body_part denotes pharynx http://purl.obolibrary.org/obo/UBERON_0006562
T12 4550-4556 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T84 47-55 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 2959-2967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 2970-2979 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 3135-3145 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T88 3175-3183 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T89 3261-3269 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 3272-3281 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 3376-3384 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T324 58-65 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T325 150-153 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T326 351-354 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T327 616-617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T328 679-684 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T329 701-702 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 832-836 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T331 889-890 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 923-924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T333 932-936 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T334 968-969 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T335 1012-1013 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T336 1067-1069 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T337 1117-1118 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T338 1671-1672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T339 2082-2089 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T340 2295-2296 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T341 2315-2322 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T342 2635-2636 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 2722-2729 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T344 2957-2958 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 3186-3191 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T346 3259-3260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T347 3308-3309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T348 3442-3443 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T349 3471-3472 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T350 3499-3506 http://purl.obolibrary.org/obo/UBERON_0001042 denotes pharynx
T351 3499-3506 http://purl.obolibrary.org/obo/UBERON_0006562 denotes pharynx
T352 3678-3679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T353 3822-3823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 4144-4147 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T355 4285-4292 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T356 4360-4365 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T357 4424-4431 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T358 4435-4436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T359 4468-4475 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T360 4634-4638 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T361 4673-4678 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T362 4690-4695 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T363 4723-4724 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 4778-4782 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T78 300-312 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T79 525-537 Chemical denotes contaminants http://purl.obolibrary.org/obo/CHEBI_143130
T80 618-630 Chemical denotes template RNA http://purl.obolibrary.org/obo/CHEBI_33699
T81 1462-1465 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T82 2413-2421 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T83 3881-3889 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T84 4012-4020 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
257 47-57 Species denotes SARS-CoV-2 Tax:2697049
261 481-483 Gene denotes pH Gene:5053
262 406-408 Gene denotes pH Gene:5053
263 899-915 Disease denotes reaction failure MESH:D006333
269 3175-3185 Species denotes SARS-CoV-2 Tax:2697049
270 2959-2979 Disease denotes SARS-CoV-2 infection MESH:C000657245
271 3261-3281 Disease denotes SARS-CoV-2 infection MESH:C000657245
272 3376-3384 Disease denotes COVID-19 MESH:C000657245
273 3565-3573 Disease denotes infected MESH:D007239

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T233 15-17 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T234 136-138 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T235 246-248 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T236 333-335 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T237 429-431 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T238 555-568 http://purl.obolibrary.org/obo/GO_0045851 denotes acidification
T239 671-673 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T240 997-999 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T241 1206-1208 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T242 1753-1755 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T243 2160-2162 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T244 2245-2247 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T245 2399-2401 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T246 2880-2882 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T247 3049-3051 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T248 3080-3082 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T249 3634-3636 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T250 3752-3754 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T251 3839-3841 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T252 3922-3924 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T253 4081-4083 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T254 4130-4132 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T255 4230-4232 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T256 4346-4348 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T257 4384-4386 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T258 4570-4572 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T259 4705-4707 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T284 0-65 Sentence denotes Application of RT-LAMP and LAMP-sequencing for SARS-CoV-2 testing
T285 66-173 Sentence denotes With its good sensitivity for samples up to CT ≈ 30, the colorimetric RT-LAMP assay has several advantages:
T286 174-245 Sentence denotes It is fast, inexpensive, and it can be evaluated without any equipment.
T287 246-494 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 495-659 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 660-937 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 938-1011 Sentence denotes It would be desirable to have a similar precaution for the RT-LAMP assay.
T291 1012-1140 Sentence denotes A multiplexed fluorescence readout might provide this (34) but comes at the expense of the simplicity of a colorimetric readout.
T292 1141-1435 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 1436-1622 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 1623-1767 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 1768-2003 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 2004-2111 Sentence denotes Thus, LAMP-sequencing could become an important part of workflows for routine testing of large populations.
T297 2112-2323 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 2324-2549 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 2550-2593 Sentence denotes There are several limitations to our study.
T300 2594-2704 Sentence denotes We used surplus RNA sample material from a diagnostic laboratory rather than newly collected clinical samples.
T301 2705-2808 Sentence denotes The criteria for testing individuals may have influenced cohort characteristics and hence our findings.
T302 2809-2980 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 2981-3192 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 3193-3393 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 3394-3593 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 3594-3696 Sentence denotes We used LAMP-sequencing to validate the RT-LAMP assay results and did not use it as a diagnostic tool.
T307 3697-3874 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 3875-3996 Sentence denotes Also, reagents such as the primer sets for the RT-LAMP assay may be subject to production-dependent quality fluctuations.
T309 3997-4110 Sentence denotes Therefore, all reagents must be precisely validated (batch control) before using an RT-LAMP assay diagnostically.
T310 4111-4225 Sentence denotes Application of the RT-LAMP assay has great potential, even more so as more sensitive primer sets become available.
T311 4226-4366 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 4367-4565 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 4566-4790 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.