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PMC:7574920 / 11871-17162 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T68 17-20 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T69 210-213 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T70 281-284 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T71 1124-1128 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T72 1174-1177 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T73 1341-1344 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T74 1786-1790 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T75 3371-3384 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T76 3371-3374 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T77 3615-3618 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T78 3774-3787 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T79 3774-3777 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T80 3934-3937 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81 3941-3944 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T82 4180-4184 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T83 4228-4232 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T84 4361-4365 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 4486-4490 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T86 4497-4501 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T87 4616-4620 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 4660-4664 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T89 4698-4701 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T90 4807-4811 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T91 4997-5001 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T92 5079-5083 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T50 544-546 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T51 766-768 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T52 1773-1781 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 1910-1912 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T54 2069-2071 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T55 2130-2132 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T56 2344-2346 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T57 2829-2831 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T58 2915-2917 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T59 4687-4695 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T111 0-7 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T112 165-166 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 288-289 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 330-331 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 362-364 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T116 445-447 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T117 484-485 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 683-684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 921-925 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 992-1000 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T121 1017-1018 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 1041-1045 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T123 1061-1062 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 1124-1128 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T125 1437-1438 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 1587-1588 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T127 1628-1629 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T128 1668-1669 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T129 1695-1696 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 1755-1756 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 1786-1790 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T132 1804-1805 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 1820-1821 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T134 2127-2128 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 2385-2386 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T136 2458-2459 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 2513-2514 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 2617-2618 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 2688-2690 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T140 2716-2717 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 2866-2867 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 3012-3013 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 3029-3030 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 3066-3070 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T145 3122-3124 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T146 3126-3127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 3208-3209 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 3277-3278 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 3340-3341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 3560-3561 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 3678-3679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 3855-3856 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 4153-4159 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T154 4180-4184 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T155 4199-4200 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 4228-4232 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T157 4361-4365 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T158 4390-4391 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 4426-4428 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T160 4486-4490 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T161 4497-4501 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T162 4539-4540 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T163 4616-4620 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T164 4660-4664 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T165 4807-4811 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T166 4884-4890 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T167 4898-4899 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 4935-4937 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T169 4997-5001 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T170 5024-5025 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 5079-5083 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T172 5176-5177 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T43 641-651 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T44 641-647 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T45 698-701 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T46 2056-2066 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T47 2056-2062 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T48 2548-2554 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T49 2559-2562 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T50 3375-3384 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T51 3778-3787 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T52 5116-5118 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
158 685-687 Gene denotes pH Gene:5053
159 641-651 Chemical denotes phenol red MESH:D010637
164 1784-1785 Gene denotes N Gene:43740575
165 1802-1803 Gene denotes N Gene:43740575
166 1773-1783 Species denotes SARS-CoV-2 Tax:2697049
167 2056-2066 Chemical denotes phenol red MESH:D010637
170 2991-2998 Species denotes patient Tax:9606
171 2548-2554 Chemical denotes phenol MESH:D019800
173 3853-3854 Gene denotes N Gene:43740575
179 4828-4832 Gene denotes RdRp Gene:43740578
180 4614-4615 Gene denotes N Gene:43740575
181 4359-4360 Gene denotes N Gene:43740575
182 4226-4227 Gene denotes N Gene:43740575
183 4687-4697 Species denotes SARS-CoV-2 Tax:2697049
187 4928-4933 Gene denotes ORF1a Gene:43740578
188 4995-4996 Gene denotes N Gene:43740575
189 5174-5175 Gene denotes N Gene:43740575

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T63 51-53 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T64 94-96 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T65 177-179 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T66 236-238 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T67 913-915 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T68 984-986 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T69 1283-1285 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T70 1309-1311 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T71 1417-1419 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T72 1458-1460 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T73 1730-1732 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T74 2274-2276 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T75 2415-2417 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T76 2473-2475 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T77 3058-3060 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T78 3246-3248 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T79 3291-3293 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T80 3304-3306 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T81 3520-3522 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T82 3632-3634 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T83 3663-3665 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T84 3796-3798 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T85 3881-3883 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T86 4118-4120 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T87 4208-4210 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T88 4307-4309 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T89 4705-4707 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T90 4861-4863 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T91 5084-5086 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T92 5197-5199 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T93 5243-5245 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T76 0-64 Sentence denotes Testing clinical RNA samples with the colorimetric RT-LAMP assay
T77 65-192 Sentence denotes To evaluate the colorimetric RT-LAMP assay, we needed to compare its sensitivity and specificity to a validated RT-qPCR method.
T78 193-317 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 318-449 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 450-726 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 727-978 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 979-1239 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 1240-1340 Sentence denotes Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.
T84 1341-1453 Sentence denotes RNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate.
T85 1454-1683 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 1684-1926 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 1927-2094 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 2095-2153 Sentence denotes Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4.
T89 2154-2186 Sentence denotes Each line represents one sample.
T90 2187-2423 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 2424-2454 Sentence denotes Each dot is one sample (well).
T92 2455-2603 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 2604-2781 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 2782-2900 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 2901-3192 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 3193-3299 Sentence denotes This suggested a detection limit of the colorimetric RT-LAMP assay corresponding to a CT ≈ 30 for RT-qPCR.
T97 3300-3495 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 3496-3579 Sentence denotes The performance of each RT-qPCR run was validated using this as a positive control.
T99 3580-3820 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 3821-3997 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 3998-4292 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 4293-4440 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 4441-4589 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 4590-4713 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 4714-4852 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 4853-5120 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 5121-5291 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.