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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
210 9774-9812 Species denotes severe acute respiratory syndrome, CoV Tax:694009
2 31-38 Species denotes Patient Tax:9606
3 44-54 Species denotes SARS-CoV-2 Tax:2697049
13 74-91 Species denotes Novel coronavirus Tax:2697049
14 93-103 Species denotes SARS-CoV-2 Tax:2697049
15 310-320 Species denotes SARS-CoV-2 Tax:2697049
16 369-376 Species denotes patient Tax:9606
17 466-476 Species denotes SARS-CoV-2 Tax:2697049
18 570-581 Species denotes Coronavirus Tax:11118
19 778-788 Species denotes SARS-CoV-2 Tax:2697049
20 192-213 Disease denotes SARS-CoV-2 infections MESH:C000657245
21 413-433 Disease denotes SARS-CoV-2 infection MESH:C000657245
28 811-824 Species denotes Coronaviruses Tax:11118
29 826-830 Species denotes CoVs Tax:11118
30 975-978 Species denotes CoV Tax:11118
31 1014-1019 Species denotes human Tax:9606
32 1198-1202 Species denotes CoVs Tax:11118
33 1236-1244 Disease denotes infected MESH:D007239
42 1395-1399 Species denotes CoVs Tax:11118
43 1401-1409 Species denotes beta-CoV Tax:694002
44 1469-1513 Species denotes severe acute respiratory syndrome (SARS)-CoV Tax:694009
45 1572-1581 Species denotes MERS)-CoV Tax:1335626
46 1621-1625 Species denotes CoVs Tax:11118
47 1659-1667 Species denotes SARS-CoV Tax:694009
48 1672-1680 Species denotes MERS-CoV Tax:1335626
49 1538-1570 Disease denotes Middle East respiratory syndrome MESH:D018352
61 1732-1746 Species denotes 2019 novel CoV Tax:2697049
62 1748-1758 Species denotes SARS-CoV-2 Tax:2697049
63 1831-1839 Species denotes patients Tax:9606
64 2077-2087 Species denotes SARS-CoV-2 Tax:2697049
65 2113-2118 Species denotes human Tax:9606
66 2204-2208 Species denotes CoVs Tax:11118
67 2267-2275 Species denotes SARS-CoV Tax:694009
68 2284-2292 Species denotes MERS-CoV Tax:1335626
69 2384-2394 Species denotes SARS-CoV-2 Tax:2697049
70 2419-2426 Species denotes patient Tax:9606
71 1850-1859 Disease denotes mortality MESH:D003643
82 2465-2472 Species denotes patient Tax:9606
83 2588-2593 Species denotes woman Tax:9606
84 2827-2833 Chemical denotes Oxygen MESH:D010100
85 2895-2901 Chemical denotes oxygen MESH:D010100
86 2509-2529 Disease denotes SARS-CoV-2 infection MESH:C000657245
87 2604-2609 Disease denotes fever MESH:D005334
88 2622-2629 Disease denotes myalgia MESH:D063806
89 2754-2774 Disease denotes SARS-CoV-2 infection MESH:C000657245
90 2808-2813 Disease denotes cough MESH:D003371
91 2956-2961 Disease denotes Fever MESH:D005334
96 3073-3080 Species denotes patient Tax:9606
97 3644-3654 Species denotes SARS-CoV-2 Tax:2697049
98 3294-3300 Chemical denotes CCL-81
99 3359-3373 Chemical denotes carbon dioxide MESH:D002245
102 4265-4279 Chemical denotes uranyl acetate MESH:C005460
103 4287-4299 Chemical denotes lead citrate
109 4658-4665 Species denotes BetaCoV Tax:694002
110 5368-5378 Species denotes SARS-CoV-2 Tax:2697049
111 5629-5636 Species denotes BetaCoV Tax:694002
112 5685-5692 Species denotes BetaCoV Tax:694002
113 4719-4727 Disease denotes infected MESH:D007239
120 6490-6496 Gene denotes ORF1ab Gene:43740578
121 6537-6542 Gene denotes ORF3a Gene:43740569
122 6513-6514 Gene denotes S Gene:43740568
123 6200-6207 Species denotes BetaCoV Tax:694002
124 6742-6749 Species denotes BetaCoV Tax:694002
125 6972-6982 Species denotes SARS-CoV-2 Tax:2697049
129 7199-7203 Species denotes CoVs Tax:11118
130 7296-7304 Species denotes beta-CoV Tax:694002
131 7386-7396 Species denotes SARS-CoV-2 Tax:2697049
136 7452-7462 Species denotes SARS-CoV-2 Tax:2697049
137 7536-7543 Species denotes patient Tax:9606
138 7642-7652 Species denotes SARS-CoV-2 Tax:2697049
139 7516-7535 Disease denotes SARS-CoV-2-infected MESH:C000657245
168 8241-8251 Species denotes SARS-CoV-2 Tax:2697049
169 8307-8317 Species denotes SARS-CoV-2 Tax:2697049
170 8626-8636 Species denotes SARS-CoV-2 Tax:2697049
171 8612-8620 Disease denotes infected MESH:D007239
174 8889-8927 Species denotes severe acute respiratory syndrome, CoV Tax:694009
175 8930-8941 Species denotes coronavirus Tax:11118
178 8999-9009 Species denotes SARS-CoV-2 Tax:2697049
179 9062-9066 Species denotes CoVs Tax:11118
184 9075-9113 Species denotes severe acute respiratory syndrome, CoV Tax:694009
185 9116-9127 Species denotes coronavirus Tax:11118
186 9129-9133 Disease denotes MERS MESH:D018352
187 9136-9168 Disease denotes Middle East respiratory syndrome MESH:D018352
196 9393-9399 Gene denotes ORF1ab Gene:43740578
197 9479-9483 Gene denotes ORF1 Gene:55354
198 9523-9529 Gene denotes ORF1ab Gene:43740578
199 9566-9572 Gene denotes ORF1ab Gene:43740578
200 9649-9654 Gene denotes ORF3a Gene:43740569
201 9692-9697 Gene denotes ORF3a Gene:43740569
202 9436-9442 Gene denotes ORF1ab Gene:43740578
203 9610-9611 Gene denotes S Gene:43740568
206 9214-9221 Species denotes BetaCoV Tax:694002
207 9288-9298 Species denotes SARS-CoV-2 Tax:2697049
211 9815-9826 Species denotes coronavirus Tax:11118

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T144 1672-1680 SP_9 denotes MERS-CoV
T143 1693-1700 NCBITaxon:species denotes species
T142 1748-1758 SP_7 denotes SARS-CoV-2
T141 1968-1973 NCBITaxon:10239 denotes virus
T140 2077-2087 SP_7 denotes SARS-CoV-2
T139 2113-2118 SP_6;NCBITaxon:9606 denotes human
T138 2119-2125 UBERON:0001005 denotes airway
T137 2126-2136 UBERON:0000483;CL:0002368 denotes epithelial
T136 2137-2142 CL:0002368 denotes cells
T135 2241-2245 SO:0000704 denotes gene
T134 2267-2275 SP_10 denotes SARS-CoV
T133 2284-2292 SP_9 denotes MERS-CoV
T132 2321-2325 GO:0040007 denotes grew
T131 2337-2341 CL_6 denotes Vero
T130 2384-2394 SP_7 denotes SARS-CoV-2
T129 2401-2405 CL_6 denotes Vero
T128 2509-2519 SP_7 denotes SARS-CoV-2
T127 2754-2764 SP_7 denotes SARS-CoV-2
T126 2790-2795 UBERON:0000004 denotes nasal
T125 2819-2825 UBERON:0007311 denotes sputum
T124 3083-3096 UBERON:0001179 denotes oropharyngeal
T123 3156-3161 NCBITaxon:10239 denotes viral
T122 3275-3279 CL_6 denotes Vero
T121 3366-3373 CHEBI:16526;CHEBI:16526 denotes dioxide
T120 3560-3564 CL_6 denotes Vero
T119 3644-3654 SP_7 denotes SARS-CoV-2
T118 3822-3826 CL_6 denotes Vero
T117 4028-4033 NCBITaxon:10239 denotes virus
T116 4045-4049 CL_6 denotes Vero
T115 4339-4347 CHEBI:10545;CHEBI:10545 denotes electron
T114 4513-4533 GO:0031410 denotes cytoplasmic vesicles
T113 4545-4564 GO:0005615 denotes extracellular space
T112 4577-4590 GO:0005886 denotes cell membrane
T148 1550-1561 UBERON:0001004 denotes respiratory
T147 1572-1576 SP_9 denotes MERS
T146 1650-1657 NCBITaxon:33208 denotes animals
T145 1659-1667 SP_10 denotes SARS-CoV
T24 44-54 SP_7 denotes SARS-CoV-2
T169 811-824 NCBITaxon:11118 denotes Coronaviruses
T168 826-830 NCBITaxon:11118 denotes CoVs
T167 850-861 NCBITaxon:99883 denotes Nidovirales
T166 912-919 NCBITaxon:10239 denotes viruses
T165 933-939 SO:0001026 denotes genome
T164 960-963 SO:0000028 denotes kbp
T163 1014-1019 SP_6;NCBITaxon:9606 denotes human
T162 1020-1029 UBERON:0000922 denotes embryonic
T161 1030-1038 UBERON:0003126 denotes tracheal
T160 1039-1044 UBERON:0000062 denotes organ
T159 1158-1169 GO:0042995 denotes projections
T158 1173-1181 CHEBI:10545;CHEBI:10545 denotes electron
T157 1223-1232 GO:0005737 denotes cytoplasm
T156 1261-1281 GO:0031410 denotes cytoplasmic vesicles
T155 1303-1308 NCBITaxon:10239 denotes virus
T154 1346-1354 GO:0006887 denotes exocytic
T153 1433-1444 NCBITaxon:10376 denotes embevovirus
T152 1446-1458 NCBITaxon:9606 denotes sarbecovirus
T151 1482-1493 UBERON:0001004 denotes respiratory
T150 1504-1508 SP_10 denotes SARS
T149 1515-1527 NCBITaxon:8296 denotes merbecovirus
T12 778-788 SP_7 denotes SARS-CoV-2
T13 725-731 SO:0001026 denotes genome
T14 673-681 CHEBI:10545;CHEBI:10545 denotes electron
T15 570-581 NCBITaxon:11118 denotes Coronavirus
T16 484-488 CL_6 denotes Vero
T17 466-476 SP_7 denotes SARS-CoV-2
T18 413-423 SP_7 denotes SARS-CoV-2
T19 330-343 UBERON:0001852 denotes oropharyngeal
T20 310-320 SP_7 denotes SARS-CoV-2
T21 192-202 SP_7 denotes SARS-CoV-2
T22 93-103 SP_7 denotes SARS-CoV-2
T23 80-91 NCBITaxon:11118 denotes coronavirus
T111 4618-4624 SO:0001026 denotes genome
T110 4643-4648 NCBITaxon:10239 denotes virus
T109 4708-4712 CL_6 denotes Vero
T108 4791-4796 NCBITaxon:10239 denotes viral
T107 5147-5152 SO:0000150 denotes reads
T106 5158-5160 SO:0000028 denotes bp
T105 5317-5322 SO:0000150 denotes reads
T104 5334-5339 SO:0000150 denotes reads
T103 5368-5378 SP_7 denotes SARS-CoV-2
T102 5379-5385 SO:0001026 denotes genome
T101 5538-5544 SO:0001026 denotes genome
T100 5576-5582 SO:0001026 denotes genome
T99 5850-5857 SO:0001026 denotes genomes
T98 6315-6321 SO:0001505 denotes genome
T97 6419-6424 SO:0000704 denotes genes
T96 6443-6448 SO:0000704 denotes genes
T95 6515-6519 SO:0000704 denotes gene
T94 6565-6569 SO:0000704 denotes gene
T93 6972-6982 SP_7 denotes SARS-CoV-2
T92 7026-7032 SO:0001026 denotes genome
T91 7053-7063 SO:0000853 denotes homologous
T90 7170-7176 SO:0001026 denotes genome
T89 7386-7396 SP_7 denotes SARS-CoV-2
T88 7452-7462 SP_7 denotes SARS-CoV-2
T87 7469-7473 CL_6 denotes Vero
T86 7516-7526 SP_7 denotes SARS-CoV-2
T85 7589-7595 SO:0001026 denotes genome
T84 7642-7652 SP_7 denotes SARS-CoV-2

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 489-493 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T2 725-731 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T3 908-911 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 933-939 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T5 1039-1044 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T6 1223-1232 Body_part denotes cytoplasm http://purl.org/sig/ont/fma/fma66835
T7 1245-1250 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T8 1261-1281 Body_part denotes cytoplasmic vesicles http://purl.org/sig/ont/fma/fma63175
T9 2126-2142 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T10 2137-2142 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T11 2241-2245 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T12 2342-2347 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T13 2406-2411 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T14 2819-2825 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T15 3001-3005 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T16 3280-3285 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17 3337-3342 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T18 3568-3573 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T19 3827-3832 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T20 3898-3903 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T21 4050-4054 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T22 4513-4533 Body_part denotes cytoplasmic vesicles http://purl.org/sig/ont/fma/fma63175
T23 4545-4564 Body_part denotes extracellular space http://purl.org/sig/ont/fma/fma70022
T24 4577-4590 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T25 4577-4581 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T26 4618-4624 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T27 4713-4718 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T28 4741-4744 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T29 4757-4760 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T30 4797-4800 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T31 4885-4888 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T32 4941-4944 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T33 5379-5385 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T34 5538-5544 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T35 5576-5582 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T36 5850-5857 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T37 6137-6147 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T38 6315-6321 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T39 6515-6519 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T40 6565-6569 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T41 6621-6632 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T42 6855-6859 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T43 7026-7032 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T44 7170-7176 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T45 7474-7479 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T46 7589-7595 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T47 8260-8264 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T48 8324-8329 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T49 8387-8391 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T50 8486-8491 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T51 8500-8504 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T52 8606-8611 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T53 8650-8654 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T54 8663-8679 Body_part denotes nuclear membrane http://purl.org/sig/ont/fma/fma63888
T55 8693-8697 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T56 8750-8769 Body_part denotes cytoplasmic vesicle http://purl.org/sig/ont/fma/fma63175
T57 8988-8995 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T58 9276-9282 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T59 9327-9331 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T60 9869-9879 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1039-1044 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T2 2819-2825 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T3 8650-8654 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T4 8693-8697 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 2604-2609 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 2622-2629 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T3 2790-2806 Phenotype denotes nasal congestion http://purl.obolibrary.org/obo/HP_0001742
T4 2808-2813 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T5 2956-2961 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 44-52 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 44-48 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T3 93-101 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 93-97 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T5 192-200 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 192-196 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T7 203-213 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T8 310-318 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 310-314 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 413-421 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 413-417 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T12 424-433 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 466-474 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 466-470 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 778-786 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 778-782 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T17 1469-1502 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T18 1504-1508 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 1659-1667 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1659-1663 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T21 1748-1756 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1748-1752 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 2077-2085 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 2077-2081 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T25 2267-2275 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 2267-2271 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T27 2384-2392 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 2384-2388 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T29 2509-2517 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 2509-2513 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T31 2520-2529 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T32 2754-2762 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 2754-2758 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 2765-2774 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T35 3644-3652 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 3644-3648 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 5368-5376 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 5368-5372 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T39 6972-6980 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 6972-6976 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T41 7386-7394 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 7386-7390 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T43 7452-7460 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 7452-7456 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T45 7516-7524 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 7516-7520 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T47 7642-7650 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 7642-7646 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T49 8144-8146 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T50 8241-8249 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 8241-8245 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T52 8307-8315 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 8307-8311 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T54 8626-8634 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 8626-8630 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T56 8882-8886 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T57 8889-8922 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T58 8999-9007 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 8999-9003 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T60 9068-9072 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T61 9075-9108 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T62 9288-9296 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 9288-9292 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 9767-9771 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 9774-9807 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 0-5 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T2 123-124 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 484-493 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero cell
T4 627-628 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 912-919 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T6 925-926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1014-1019 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T8 1039-1044 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T9 1245-1250 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T10 1303-1308 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T11 1637-1638 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1650-1657 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T13 1760-1763 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T14 1776-1777 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1968-1973 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T16 2113-2118 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T17 2119-2125 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T18 2126-2136 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T19 2137-2142 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T20 2241-2245 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T21 2337-2341 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T22 2337-2341 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T23 2342-2347 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T24 2348-2350 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T25 2401-2405 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T26 2401-2405 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T27 2406-2411 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T28 2417-2418 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 2574-2575 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 2576-2578 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T31 2641-2643 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T32 2976-2979 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T33 3275-3279 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T34 3275-3279 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T35 3280-3285 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T36 3324-3342 http://purl.obolibrary.org/obo/CL_0000010 denotes cultured the cells
T37 3354-3355 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 3560-3573 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T39 3822-3826 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T40 3822-3826 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T41 3827-3832 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T42 3898-3903 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T43 4004-4005 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T44 4028-4033 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T45 4045-4054 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero cell
T46 4162-4165 http://purl.obolibrary.org/obo/CLO_0008845 denotes RMC
T47 4173-4176 http://purl.obolibrary.org/obo/CLO_0008845 denotes RMC
T48 4324-4325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 4577-4581 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T50 4582-4590 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T51 4643-4648 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T52 4708-4712 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T53 4708-4712 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T54 4713-4718 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T55 5124-5125 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5366-5367 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5447-5448 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 5471-5473 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T59 5911-5912 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 6093-6094 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 6419-6424 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T62 6443-6448 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T63 6515-6519 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 6565-6569 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T65 6855-6859 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T66 7247-7248 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 7294-7295 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 7469-7473 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T69 7469-7473 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T70 7474-7479 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T71 7958-7960 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T72 8056-8058 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T73 8191-8193 http://purl.obolibrary.org/obo/CLO_0008426 denotes PG
T74 8206-8208 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T75 8255-8264 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero cell
T76 8319-8323 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T77 8319-8323 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T78 8324-8329 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T79 8379-8380 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T80 8382-8391 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero cell
T81 8423-8424 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T82 8486-8491 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T83 8495-8504 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero cell
T84 8601-8605 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T85 8601-8605 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T86 8606-8611 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T87 8650-8654 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T88 8650-8654 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T89 8671-8679 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T90 8693-8697 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T91 8693-8697 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T92 8712-8717 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T93 8780-8785 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T94 8838-8843 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T95 9286-9287 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 9327-9331 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T97 9347-9349 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T98 9355-9357 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T99 9610-9614 http://purl.obolibrary.org/obo/CLO_0008954 denotes S C
T100 9710-9713 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T101 9741-9742 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T102 9760-9762 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T103 9864-9866 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 651-656 Chemical denotes crown http://purl.obolibrary.org/obo/CHEBI_37409
T2 673-681 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T3 1106-1112 Chemical denotes corona http://purl.obolibrary.org/obo/CHEBI_37409
T4 1121-1126 Chemical denotes crown http://purl.obolibrary.org/obo/CHEBI_37409
T5 1173-1181 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T6 1401-1405 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T7 2199-2203 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T8 2827-2833 Chemical denotes Oxygen http://purl.obolibrary.org/obo/CHEBI_15379
T9 2895-2901 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T10 3294-3297 Chemical denotes CCL http://purl.obolibrary.org/obo/CHEBI_3478
T11 3359-3373 Chemical denotes carbon dioxide http://purl.obolibrary.org/obo/CHEBI_16526
T12 3359-3365 Chemical denotes carbon http://purl.obolibrary.org/obo/CHEBI_27594|http://purl.obolibrary.org/obo/CHEBI_33415
T14 3794-3796 Chemical denotes MA http://purl.obolibrary.org/obo/CHEBI_474859|http://purl.obolibrary.org/obo/CHEBI_73610|http://purl.obolibrary.org/obo/CHEBI_90325
T17 4166-4168 Chemical denotes MT http://purl.obolibrary.org/obo/CHEBI_73614
T18 4272-4279 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T20 4292-4299 Chemical denotes citrate http://purl.obolibrary.org/obo/CHEBI_16947|http://purl.obolibrary.org/obo/CHEBI_50744|http://purl.obolibrary.org/obo/CHEBI_133748
T23 4339-4347 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T24 4394-4396 Chemical denotes MA http://purl.obolibrary.org/obo/CHEBI_474859|http://purl.obolibrary.org/obo/CHEBI_73610|http://purl.obolibrary.org/obo/CHEBI_90325
T27 4438-4443 Chemical denotes crown http://purl.obolibrary.org/obo/CHEBI_37409
T28 5307-5312 Chemical denotes bases http://purl.obolibrary.org/obo/CHEBI_22695
T29 5583-5587 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T30 6137-6147 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T31 6621-6632 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T32 6621-6626 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T33 6627-6632 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T34 7296-7300 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T35 7816-7824 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T36 7958-7960 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T37 8024-8026 Chemical denotes GW http://purl.obolibrary.org/obo/CHEBI_73921
T38 8056-8058 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T39 8075-8077 Chemical denotes MW http://purl.obolibrary.org/obo/CHEBI_74709
T40 8182-8184 Chemical denotes MW http://purl.obolibrary.org/obo/CHEBI_74709
T41 8191-8193 Chemical denotes PG http://purl.obolibrary.org/obo/CHEBI_14336|http://purl.obolibrary.org/obo/CHEBI_18208|http://purl.obolibrary.org/obo/CHEBI_61695|http://purl.obolibrary.org/obo/CHEBI_64716|http://purl.obolibrary.org/obo/CHEBI_64961
T46 8206-8208 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T47 8278-8286 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T48 8572-8580 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T49 8859-8864 Chemical denotes crown http://purl.obolibrary.org/obo/CHEBI_37409
T50 9057-9061 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T51 9338-9341 Chemical denotes Alt http://purl.obolibrary.org/obo/CHEBI_37708
T52 9347-9349 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T54 9351-9354 Chemical denotes Alt http://purl.obolibrary.org/obo/CHEBI_37708
T55 9355-9357 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T57 9380-9383 Chemical denotes Alt http://purl.obolibrary.org/obo/CHEBI_37708
T58 9407-9410 Chemical denotes Met http://purl.obolibrary.org/obo/CHEBI_16044|http://purl.obolibrary.org/obo/CHEBI_16643|http://purl.obolibrary.org/obo/CHEBI_16811
T61 9412-9415 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T63 9450-9453 Chemical denotes Asn http://purl.obolibrary.org/obo/CHEBI_17196|http://purl.obolibrary.org/obo/CHEBI_22653|http://purl.obolibrary.org/obo/CHEBI_50347
T66 9455-9458 Chemical denotes Asn http://purl.obolibrary.org/obo/CHEBI_17196|http://purl.obolibrary.org/obo/CHEBI_22653|http://purl.obolibrary.org/obo/CHEBI_50347
T69 9493-9496 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T71 9498-9501 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T73 9537-9540 Chemical denotes Tyr http://purl.obolibrary.org/obo/CHEBI_17895|http://purl.obolibrary.org/obo/CHEBI_18186|http://purl.obolibrary.org/obo/CHEBI_46858
T76 9542-9545 Chemical denotes Tyr http://purl.obolibrary.org/obo/CHEBI_17895|http://purl.obolibrary.org/obo/CHEBI_18186|http://purl.obolibrary.org/obo/CHEBI_46858
T79 9580-9583 Chemical denotes Thr http://purl.obolibrary.org/obo/CHEBI_16857|http://purl.obolibrary.org/obo/CHEBI_30013
T81 9585-9588 Chemical denotes Met http://purl.obolibrary.org/obo/CHEBI_16044|http://purl.obolibrary.org/obo/CHEBI_16643|http://purl.obolibrary.org/obo/CHEBI_16811
T84 9619-9622 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T86 9624-9627 Chemical denotes Trp http://purl.obolibrary.org/obo/CHEBI_16828|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_29954
T89 9662-9665 Chemical denotes Trp http://purl.obolibrary.org/obo/CHEBI_16828|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_29954
T92 9667-9670 Chemical denotes Leu http://purl.obolibrary.org/obo/CHEBI_15603|http://purl.obolibrary.org/obo/CHEBI_25017|http://purl.obolibrary.org/obo/CHEBI_30006
T95 9705-9708 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T96 9710-9713 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T98 9744-9747 Chemical denotes Leu http://purl.obolibrary.org/obo/CHEBI_15603|http://purl.obolibrary.org/obo/CHEBI_25017|http://purl.obolibrary.org/obo/CHEBI_30006
T101 9845-9848 Chemical denotes Alt http://purl.obolibrary.org/obo/CHEBI_37708
T102 9864-9866 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T104 9869-9879 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T105 9869-9874 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T106 9875-9879 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3156-3171 http://purl.obolibrary.org/obo/GO_0046794 denotes viral transport
T2 3162-3171 http://purl.obolibrary.org/obo/GO_0006810 denotes transport

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-63 Sentence denotes Virus Isolation from the First Patient with SARS-CoV-2 in Korea
T2 65-73 Sentence denotes Abstract
T3 74-297 Sentence denotes Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now.
T4 298-443 Sentence denotes We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea.
T5 444-569 Sentence denotes Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample.
T6 570-693 Sentence denotes Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy.
T7 694-809 Sentence denotes Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.
T8 811-974 Sentence denotes Coronaviruses (CoVs), within the order Nidovirales, are enveloped, single-strand, positive-sense RNA viruses with a large genome of approximately 30 kbp in length.
T9 975-1193 Sentence denotes CoV was cultured for the first time in human embryonic tracheal organ cultures by Tyrrell and Bynoe in 1965,1 and it was named as ‘corona’ due to crown-like appearance of the surface projections on electron microscopy.
T10 1194-1373 Sentence denotes All CoVs develop only in the cytoplasm of infected cells, bud into cytoplasmic vesicles, and then extrude in virus particles of 70–80 nm in diameter by exocytic secretory pathway.
T11 1374-1612 Sentence denotes Among four genera of CoVs, beta-CoV includes five subgenus—embevovirus, sarbecovirus including severe acute respiratory syndrome (SARS)-CoV, merbecovirus including Middle East respiratory syndrome (MERS)-CoV, nobecovirus, and hibecovirus.
T12 1613-1710 Sentence denotes Because CoVs can infect a variety of animals, SARS-CoV and MERS-CoV crossed the species barriers.
T13 1711-2076 Sentence denotes Since December 2019, 2019 novel CoV (SARS-CoV-2) has been making a large outbreak involving 49,053 laboratory-confirmed patients and 1,383 mortality in 25 countries including Korea until February 14, 2020.2 In the outbreak situation, isolation of causative virus is indispensable for developing and evaluating diagnostic tools, therapeutics, and vaccine candidates.
T14 2077-2460 Sentence denotes SARS-CoV-2 was first isolated using human airway epithelial cells and it was classified into the subgenus sarbecovirus of beta-CoVs by phylogenetic analyses of the gene sequences.3 Both the SARS-CoV and the MERS-CoV were initially isolated and grew readily in Vero cells.45 Here, we report the isolation of SARS-CoV-2 using Vero cells from a patient entering Korea from Wuhan, China.
T15 2461-2713 Sentence denotes The patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea is published previously.6 Briefly, a 35-year-old woman developed fever, chill, and myalgia on January 18, 2020, and arrived at the Incheon airport from Wuhan on the next day.
T16 2714-2826 Sentence denotes After laboratory-confirmed diagnosis of SARS-CoV-2 infection, she developed nasal congestion, cough, and sputum.
T17 2827-2955 Sentence denotes Oxygen supplementation was started on day 4 of her illness, and her oxygen requirement increased to 6 L/min on day 7 of illness.
T18 2956-3068 Sentence denotes Fever persisted for ten days and her maximum body temperature during her illness was 38.9°C on day 7 of illness.
T19 3069-3246 Sentence denotes The patient's oropharyngeal samples were obtained by using UTM™ kit containing 1 mL of viral transport media (Copan Diagnostics Inc., Murrieta, CA, USA) on day 7 of her illness.
T20 3247-3385 Sentence denotes We inoculated monolayers of Vero cells (ATCC ® CCL-81™) with the samples and cultured the cells at 37°C in a 5% carbon dioxide atmosphere.
T21 3386-4007 Sentence denotes Until 5 days after inoculation, cytopathic effects were not distinct, which is compatible with the previous findings that no specific cytopathic effects were observed in the Vero E6 cells until 6 days after inoculation in the report about first isolation of SARS-CoV-2.3 Five days after inoculation, we did blind passage of culture supernatant into T-25 culture flask (ThermoFisher Scientific Inc., Waltham, MA, USA) with monolayers of Vero cells, and cytopathic effects consisting of rounding and detachment of cells were observed in the whole area of the T-25 flask 3 days after the first blind passage (Fig. 1A and B).
T22 4008-4214 Sentence denotes In order to observe virus particles, Vero cell monolayer showing the cytopathic effects was fixed as previously described.7 It was cut on ultramicrotome (RMC MT-XL; RMC Boeckeler, Tucson, AZ, USA) at 65 nm.
T23 4215-4412 Sentence denotes Ultrathin sections were stained with saturated 4% uranyl acetate and 1% lead citrate before examination with a transmission electron microscope (JEM-1400; JEOL USA Inc., Peabody, MA, USA) at 80 kV.
T24 4413-4607 Sentence denotes Spherical particles with crown-like spikes ranging 66 to 81 nm in diameter were observed within the cytoplasmic vesicles and in the extracellular space adjacent to cell membrane (Fig. 1C and D).
T25 4608-4756 Sentence denotes For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction.
T26 4757-4884 Sentence denotes RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions.
T27 4885-4961 Sentence denotes RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No.
T28 4962-5041 Sentence denotes 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol.
T29 5042-5323 Sentence denotes Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads.
T30 5324-5710 Sentence denotes Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020.
T31 5711-5835 Sentence denotes The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org).
T32 5836-6169 Sentence denotes The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14
T33 6170-6247 Sentence denotes Next-generation sequencing of BetaCoV/Korea/SNU01/2020 (GenBank accession no.
T34 6248-6352 Sentence denotes MT039890) revealed 9 mutations compared to the NC_045512 reference genome isolated from Wuhan (Table 1).
T35 6353-6461 Sentence denotes Most of the mutations in our isolate consisted of 70% alternative genes and 30% reference genes (NC_045512).
T36 6462-6570 Sentence denotes Five variants were found in ORF1ab, one variant in S gene, two variants in ORF3a, and one variant in E gene.
T37 6571-6633 Sentence denotes Of the nine mutations, six also showed changes in amino acids.
T38 6634-6825 Sentence denotes When comparing our isolate with the one isolated from the Korea Centers for Disease Control and Prevention (BetaCoV/Korea/KCDC03/2020), 12 variants including the above 9 mutations were found.
T39 6826-7011 Sentence denotes These mutations may occur by cell culture-adaptation in that our culture isolate was obtained after first blind passage, or by micro-evolution of SARS-CoV-2 before acquisition in Wuhan.
T40 7012-7125 Sentence denotes Because those genome sequences are quite homologous each other, it is difficult to validate these two hypothesis.
T41 7126-7243 Sentence denotes The phylogenetic tree was analyzed using 37 genome information including CoVs isolated from Korea and Wuhan (Fig. 2).
T42 7244-7427 Sentence denotes As a result, it was confirmed that our isolate is a beta-CoV belonging to the subgenus sarbecovirus, and that it closely clustered with other SARS-CoV-2 isolated from Korea and Wuhan.
T43 7428-7553 Sentence denotes In summary, we isolated SARS-CoV-2 using Vero cells from the first laboratory-confirmed SARS-CoV-2-infected patient in Korea.
T44 7554-7680 Sentence denotes Phylogenetic analyses of the whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan, China.
T45 7682-7697 Sentence denotes ACKNOWLEDGMENTS
T46 7698-7836 Sentence denotes We thank Eun Kyung Choi (Department of Pathology, Seoul National University Hospital) for her technical assistance in electron microscopy.
T47 7837-7848 Sentence denotes Disclosure:
T48 7849-7913 Sentence denotes The authors have no potential conflicts of interest to disclose.
T49 7914-7935 Sentence denotes Author Contributions:
T50 7936-7954 Sentence denotes Conceptualization:
T51 7955-7970 Sentence denotes Oh MD, Park WB.
T52 7971-7985 Sentence denotes Data curation:
T53 7986-8035 Sentence denotes Park WB, Kwon NJ, Choi SJ, Yun J, Lee GW, Kim JY.
T54 8036-8052 Sentence denotes Formal analysis:
T55 8053-8094 Sentence denotes Oh MD, Park WB, Seong MW, Kim NJ, Seo JS.
T56 8095-8120 Sentence denotes Writing - original draft:
T57 8121-8147 Sentence denotes Park WB, Kwon NJ, Kang CK.
T58 8148-8175 Sentence denotes Writing - review & editing:
T59 8176-8209 Sentence denotes Seong MW, Choe PG, Kim NJ, Oh MD.
T60 8211-8318 Sentence denotes Fig. 1 Cytopathic effects of SARS-CoV-2 in Vero cell cultures and electron microscopy image of SARS-CoV-2.
T61 8319-8637 Sentence denotes Vero cells were inoculated with oropharyngeal swab sample. (A) Vero cell cultures in negative control. (B) Cytopathic effects consisting of rounding and detachment of cells in Vero cell cultures 3 days after the first blind passage. (C, D) Transmission electron microscopy image of Vero cells infected with SARS-CoV-2.
T62 8638-8801 Sentence denotes White arrow head denotes nuclear membrane, black arrow head extracellular virus particles, and thin black arrow cytoplasmic vesicle including virus components (C).
T63 8802-8881 Sentence denotes Thick black arrow denotes magnified virus particles with crown-like spikes (D).
T64 8882-8942 Sentence denotes SARS = severe acute respiratory syndrome, CoV = coronavirus.
T65 8943-9067 Sentence denotes Fig. 2 Phylogenetic analysis of full-length genomes of SARS-CoV-2 including our isolate and other representative beta-CoVs.
T66 9068-9169 Sentence denotes SARS = severe acute respiratory syndrome, CoV = coronavirus, MERS = Middle East respiratory syndrome.
T67 9170-9316 Sentence denotes Table 1 Genetic variations of our isolate (BetaCoV/Korea/SNU01/2020) compared to the NC_045512 reference genome of a SARS-CoV-2 isolated in Wuhan
T68 9317-9386 Sentence denotes Position Gene Ref Alt Ref AA Alt AA Total depth Ref, % Alt, %
T69 9387-9429 Sentence denotes 2971 ORF1ab G T Met Ile 7917 31 69
T70 9430-9471 Sentence denotes 6031 ORF1ab C T Asn Asn 7966 5 95
T71 9472-9515 Sentence denotes 12115 ORF1ab C T Ser Ser 7875 33 67
T72 9516-9558 Sentence denotes 15597 ORF1ab T C Tyr Tyr 7977 4 96
T73 9559-9602 Sentence denotes 20936 ORF1ab C T Thr Met 7984 31 69
T74 9603-9641 Sentence denotes 22224 S C G Ser Trp 7993 33 67
T75 9642-9684 Sentence denotes 25775 ORF3a G T Trp Leu 7995 32 68
T76 9685-9727 Sentence denotes 26144 ORF3a G T Gly Val 7885 0 100
T77 9728-9766 Sentence denotes 26354 E T A Leu His 7609 36 64
T78 9767-9880 Sentence denotes SARS = severe acute respiratory syndrome, CoV = coronavirus, Ref = reference, Alt = alternative, AA = amino acid.