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PMC:7033720 / 7231-21745 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
90 2021-2024 Gene denotes AST Gene:26503
91 2128-2132 Chemical denotes UREA MESH:D014508
98 2249-2252 Gene denotes AST Gene:26503
99 2313-2323 Chemical denotes creatinine MESH:D003404
100 2352-2362 Chemical denotes creatinine MESH:D003404
101 2364-2368 Chemical denotes UREA MESH:D014508
102 2371-2375 Chemical denotes Urea MESH:D014508
103 2376-2384 Chemical denotes nitrogen MESH:D009584
128 374-378 Gene denotes a 21 Gene:28922
129 94-102 Species denotes patients Tax:9606
130 147-154 Species denotes Patient Tax:9606
131 360-367 Species denotes Patient Tax:9606
132 624-634 Species denotes outpatient Tax:9606
133 767-775 Species denotes patients Tax:9606
134 1054-1061 Species denotes patient Tax:9606
135 1343-1350 Species denotes patient Tax:9606
136 1439-1447 Species denotes patients Tax:9606
137 1571-1578 Species denotes patient Tax:9606
138 1585-1592 Species denotes patient Tax:9606
139 1149-1153 Chemical denotes SpO2
140 1162-1168 Chemical denotes oxygen MESH:D010100
141 84-93 Disease denotes pneumonia MESH:D011014
142 227-232 Disease denotes fever MESH:D005334
143 263-268 Disease denotes cough MESH:D003371
144 425-438 Disease denotes febrile cough MESH:D003371
145 448-453 Disease denotes fever MESH:D005334
146 883-899 Disease denotes viral infections MESH:D001102
147 977-986 Disease denotes infection MESH:D007239
148 1120-1139 Disease denotes shortness of breath MESH:D004417
149 1213-1229 Disease denotes pleural effusion MESH:D010996
150 1369-1395 Disease denotes Type I respiratory failure MESH:D012131
151 1474-1493 Disease denotes Infectious Diseases MESH:D003141
158 3369-3373 Gene denotes SAR1 Gene:56681
159 3309-3317 Species denotes SARS-CoV Tax:694009
160 3441-3448 Species denotes patient Tax:9606
161 3489-3496 Species denotes patient Tax:9606
162 3533-3541 Species denotes patients Tax:9606
163 3246-3255 Disease denotes pneumonia MESH:D011014
174 2527-2535 Species denotes patients Tax:9606
175 2625-2640 Species denotes Influenza virus Tax:11308
176 2642-2669 Species denotes Respiratory syncytial virus Tax:12814
177 2671-2681 Species denotes Adenovirus Tax:10508
178 2844-2852 Species denotes SARS-CoV Tax:694009
179 3140-3148 Species denotes SARS-CoV Tax:694009
180 2479-2490 Species denotes respiratory Tax:12814
181 2592-2603 Species denotes respiratory Tax:12814
182 2711-2720 Disease denotes pneumonia MESH:D011014
183 2722-2745 Disease denotes Chlamydophila pneumonia MESH:D023521
187 4367-4374 Species denotes patient Tax:9606
188 4449-4456 Species denotes patient Tax:9606
189 4197-4206 Disease denotes pneumonia MESH:D011014
193 3953-3964 Species denotes coronavirus Tax:694448
194 3973-3981 Species denotes SARS-CoV Tax:694009
195 3932-3941 Disease denotes pneumonia MESH:D011014
203 5225-5238 Species denotes coronaviruses Tax:11118
204 5268-5273 Species denotes human Tax:9606
205 5500-5517 Species denotes Capnocytophaga sp Tax:44737
206 5522-5536 Species denotes Veillonella sp Tax:1926307
207 5654-5665 Species denotes coronavirus Tax:694448
208 5830-5833 Species denotes CoV Tax:11118
209 5883-5886 Species denotes CoV Tax:11118
234 7921-7927 Species denotes b A 15 Tax:447219
235 8130-8136 Species denotes b A 20 Tax:447224
236 6992-6997 CellLine denotes WHU01 CVCL:9726
237 7054-7059 CellLine denotes WHU01 CVCL:9726
238 7120-7125 CellLine denotes WHU01 CVCL:9726
239 7184-7189 CellLine denotes WHU01 CVCL:9726
240 7248-7253 CellLine denotes WHU01 CVCL:9726
241 7311-7316 CellLine denotes WHU01 CVCL:9726
242 7375-7380 CellLine denotes WHU01 CVCL:9726
243 7439-7444 CellLine denotes WHU01 CVCL:9726
244 7502-7507 CellLine denotes WHU01 CVCL:9726
245 7567-7572 CellLine denotes WHU01 CVCL:9726
246 7630-7635 CellLine denotes WHU01 CVCL:9726
247 7693-7698 CellLine denotes WHU01 CVCL:9726
248 7775-7780 CellLine denotes WHU01 CVCL:9726
249 7843-7848 CellLine denotes WHU01 CVCL:9726
250 7914-7919 CellLine denotes WHU01 CVCL:9726
251 7983-7988 CellLine denotes WHU01 CVCL:9726
252 8053-8058 CellLine denotes WHU01 CVCL:9726
253 8108-8128 CellLine denotes 19.10 1.90E-47 WHU01 CVCL:6820
254 8192-8197 CellLine denotes WHU01 CVCL:9726
255 8259-8264 CellLine denotes WHU01 CVCL:9726
256 8327-8332 CellLine denotes WHU01 CVCL:9726
257 8390-8395 CellLine denotes WHU01 CVCL:9726
259 6847-6852 CellLine denotes WHU01 CVCL:9726
269 6276-6284 Species denotes patients Tax:9606
270 6311-6314 Species denotes CoV Tax:11118
271 6372-6381 Species denotes 2019-nCoV Tax:2697049
272 6742-6753 Species denotes coronaviral Tax:11118
273 6787-6795 Species denotes patients Tax:9606
274 6290-6298 Disease denotes infected MESH:D007239
275 6188-6196 CellLine denotes MN988668 CVCL:U508
276 6201-6209 CellLine denotes MN988669 CVCL:U508
277 6389-6394 CellLine denotes WHU01 CVCL:9726
287 10522-10527 Gene denotes ORF1b Gene:43740578
288 10411-10415 Species denotes CoVs Tax:11118
289 10436-10445 Species denotes 2019-nCoV Tax:2697049
290 10478-10482 Species denotes CoVs Tax:11118
291 10586-10591 Species denotes human Tax:9606
292 10693-10697 Species denotes CoVs Tax:11118
293 10815-10823 Species denotes SARS-CoV Tax:694009
294 10999-11003 Species denotes CoVs Tax:11118
295 11177-11186 Species denotes SARS CoVs Tax:694009
315 10038-10043 Gene denotes ORF1b Gene:43740578
316 9444-9453 Species denotes 2019-nCoV Tax:2697049
317 9565-9574 Species denotes 2019-nCoV Tax:2697049
318 9587-9591 Species denotes CoVs Tax:11118
319 9620-9634 Species denotes Horseshoe bats Tax:49442
320 9689-9704 Species denotes bat coronavirus Tax:1508220
321 9814-9817 Species denotes CoV Tax:11118
322 9925-9930 Species denotes human Tax:9606
323 9931-9934 Species denotes CoV Tax:11118
324 9946-9954 Species denotes SARS-CoV Tax:694009
325 9971-9980 Species denotes 2019-nCoV Tax:2697049
326 10005-10018 Species denotes Coronaviridae Tax:11118
327 10082-10086 Species denotes CoVs Tax:11118
328 10157-10166 Species denotes 2019-nCoV Tax:2697049
329 10190-10203 Species denotes β-coronavirus Tax:694002
330 10274-10278 Species denotes CoVs Tax:11118
331 10332-10346 Species denotes horseshoe bats Tax:49442
332 9607-9618 Species denotes Rhinolophus Tax:89399
333 10315-10326 Species denotes Rhinolophus Tax:89399
344 11508-11513 Gene denotes ORF1b Gene:43740578
345 11261-11270 Species denotes 2019-nCoV Tax:2697049
346 11281-11285 Species denotes CoVs Tax:11118
347 11420-11429 Species denotes 2019-nCoV Tax:2697049
348 11466-11470 Species denotes CoVs Tax:11118
349 11650-11669 Species denotes Rhinolophus affinis Tax:59477
350 11860-11879 Species denotes Rhinolophus sinicus Tax:89399
351 11982-11991 Species denotes 2019-nCoV Tax:2697049
352 12291-12297 Species denotes humans Tax:9606
353 11487-11498 Species denotes Rhinolophus Tax:89399
365 12644-12649 Gene denotes ORF1a Gene:43740578
366 12651-12652 Gene denotes S Gene:43740568
367 12658-12659 Gene denotes N Gene:43740575
368 12678-12683 Gene denotes ORF1b Gene:43740578
369 12693-12698 Gene denotes ORF1b Gene:43740578
370 12447-12456 Species denotes 2019-nCoV Tax:2697049
371 12484-12488 Species denotes CoVs Tax:11118
372 12565-12574 Species denotes 2019-nCoV Tax:2697049
373 12848-12857 Species denotes 2019-nCoV Tax:2697049
374 12893-12901 Species denotes SARS-CoV Tax:694009
375 12959-12968 Species denotes 2019-nCoV Tax:2697049
385 13201-13210 Species denotes novel CoV Tax:2697049
386 13220-13228 Species denotes patients Tax:9606
387 13829-13834 Species denotes prion Tax:36469
388 13953-13962 Species denotes 2019-nCoV Tax:2697049
389 14012-14015 Species denotes CoV Tax:11118
390 14083-14089 Species denotes humans Tax:9606
391 13242-13251 Disease denotes pneumonia MESH:D011014
392 13900-13908 Disease denotes infected MESH:D007239
393 14136-14144 Disease denotes zoonotic MESH:D015047

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T42 287-293 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T43 485-491 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T44 745-750 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T45 820-826 Body_part denotes pleura http://purl.org/sig/ont/fma/fma9583
T46 844-848 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T47 918-923 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T48 1105-1111 Body_part denotes mental http://purl.org/sig/ont/fma/fma264279
T49 1237-1246 Body_part denotes left lung http://purl.org/sig/ont/fma/fma7310
T50 1854-1865 Body_part denotes Neutrophils http://purl.org/sig/ont/fma/fma62860
T51 1894-1906 Body_part denotes T lymphocyte http://purl.org/sig/ont/fma/fma62870
T52 1961-1969 Body_part denotes Platelet http://purl.org/sig/ont/fma/fma62851
T53 2223-2230 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T54 2391-2402 Body_part denotes haemoglobin http://purl.org/sig/ont/fma/fma62293
T55 2445-2450 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T56 2495-2500 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T57 2808-2811 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T58 3279-3282 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T59 3714-3720 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T60 4000-4003 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 4212-4215 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 5095-5101 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T63 5396-5400 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T64 5887-5893 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T65 5934-5940 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T66 6016-6026 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T67 6113-6119 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T68 6475-6481 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T69 6572-6578 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T70 6773-6778 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T71 6812-6822 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T72 6863-6870 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T73 9429-9436 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T74 9531-9537 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T75 9666-9676 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T76 9771-9775 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T77 9787-9797 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T78 10044-10051 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T79 10528-10535 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T80 10715-10721 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T81 10869-10875 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T82 11045-11055 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T83 11133-11137 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T84 11192-11196 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 11325-11335 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T86 11514-11518 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T87 11573-11583 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T88 11616-11620 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T89 11771-11781 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T90 11823-11833 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T91 12119-12126 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T92 12361-12365 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T93 12684-12688 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T94 12699-12703 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T95 12828-12834 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T96 13121-13127 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T97 13644-13657 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T98 13644-13647 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 13771-13774 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T100 14387-14390 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 287-293 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T4 485-491 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 745-750 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T6 820-826 Body_part denotes pleura http://purl.obolibrary.org/obo/UBERON_0000977
T7 844-854 Body_part denotes lung field http://purl.obolibrary.org/obo/UBERON_0022361
T8 844-848 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T9 1213-1229 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175
T10 1237-1246 Body_part denotes left lung http://purl.obolibrary.org/obo/UBERON_0002168
T11 1242-1246 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 1309-1318 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106
T13 2445-2450 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T14 2495-2500 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T15 5396-5400 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T9 84-93 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T10 883-899 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T11 977-986 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 1376-1395 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T13 1474-1484 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T14 2062-2064 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T15 2081-2083 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T16 2283-2285 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T17 2305-2307 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T18 2625-2634 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 2700-2720 Disease denotes Mycoplasma pneumonia http://purl.obolibrary.org/obo/MONDO_0005867
T20 2711-2720 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T21 2736-2745 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T22 2751-2761 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T23 2844-2852 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 3140-3148 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 3246-3255 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T26 3309-3317 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 3932-3941 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T28 3973-3981 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 4197-4206 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T30 9946-9954 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 10815-10823 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 10989-10993 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 11177-11181 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 12893-12901 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 13242-13251 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T36 14028-14032 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T52 161-162 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 175-179 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T54 175-179 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T55 374-378 http://purl.obolibrary.org/obo/CLO_0053711 denotes a 21
T56 388-394 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T57 505-506 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 681-685 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T59 745-750 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T60 820-826 http://purl.obolibrary.org/obo/UBERON_0000977 denotes pleura
T61 844-848 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T62 844-848 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T63 849-854 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T64 863-865 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T65 918-923 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T66 1181-1182 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 1213-1229 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion
T68 1237-1246 http://purl.obolibrary.org/obo/UBERON_0002168 denotes left lung
T69 1737-1741 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T70 1819-1823 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T71 1933-1935 http://purl.obolibrary.org/obo/CLO_0003622 denotes Hb
T72 2038-2040 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T73 2059-2061 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T74 2070-2072 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T75 2073-2075 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T76 2084-2086 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T77 2092-2094 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T78 2308-2310 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T79 2331-2333 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T80 2386-2388 http://purl.obolibrary.org/obo/CLO_0003622 denotes Hb
T81 2445-2450 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T82 2445-2450 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T83 2495-2500 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T84 2495-2500 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T85 2582-2587 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T86 2635-2640 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T87 2664-2669 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T88 2904-2916 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T89 3068-3073 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T90 3276-3277 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T91 3415-3417 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T92 3457-3461 http://purl.obolibrary.org/obo/CLO_0050509 denotes 2, 7
T93 3471-3473 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T94 3577-3578 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T95 3951-3952 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 4209-4210 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 4277-4282 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T98 4305-4309 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3, 5
T99 4317-4319 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T100 4349-4351 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T101 4407-4409 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T102 4419-4421 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T103 4461-4462 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T104 4970-4971 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 5124-5125 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T106 5268-5273 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T107 5580-5588 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T108 5787-5788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 5793-5795 http://purl.obolibrary.org/obo/CLO_0007074 denotes kb
T110 5793-5795 http://purl.obolibrary.org/obo/CLO_0051988 denotes kb
T111 6509-6518 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T112 6735-6741 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T113 6773-6778 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T114 7007-7012 http://purl.obolibrary.org/obo/CLO_0001012 denotes 221 1
T115 7019-7021 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T116 7063-7064 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T117 7081-7082 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T118 7129-7130 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T119 7147-7148 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T120 7181-7183 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T121 7207-7208 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T122 7257-7259 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T123 7257-7259 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T124 7257-7259 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T125 7272-7274 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T126 7277-7279 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T127 7277-7279 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T128 7277-7279 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T129 7462-7463 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T130 7511-7512 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T131 7529-7530 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T132 7590-7591 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 7852-7854 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T134 7852-7854 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T135 7852-7854 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T136 7871-7873 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T137 7876-7878 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T138 7876-7878 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T139 7876-7878 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T140 7923-7924 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 7945-7946 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T142 8010-8011 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T143 8132-8133 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T144 8154-8155 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 8200-8201 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T146 8222-8223 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T147 8267-8268 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T148 8289-8293 http://purl.obolibrary.org/obo/CLO_0001599 denotes A 54
T149 8333-8336 http://purl.obolibrary.org/obo/CLO_0008954 denotes S C
T150 8353-8354 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T151 8406-8407 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T152 8428-8429 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 8538-8539 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T154 8556-8557 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T155 8604-8605 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T156 8622-8623 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 8656-8658 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T158 8683-8688 http://purl.obolibrary.org/obo/CLO_0002087 denotes C 129
T159 8722-8723 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T160 8744-8745 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T161 8810-8811 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 8950-8951 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T163 8956-8959 http://purl.obolibrary.org/obo/CLO_0001311 denotes 356
T164 9070-9071 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 9092-9093 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T166 9146-9147 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 9168-9169 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 9326-9329 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T169 9630-9634 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T170 9689-9692 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T171 9771-9775 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T172 9810-9813 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T173 9825-9828 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T174 9844-9847 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T175 9925-9930 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T176 10232-10233 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 10267-10270 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T178 10342-10346 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T179 10417-10418 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T180 10586-10591 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T181 10603-10610 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T182 10712-10713 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T183 10752-10759 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T184 10796-10799 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T185 10827-10828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 10966-10973 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T187 11073-11078 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T188 11133-11137 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T189 11192-11196 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T190 11224-11225 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 11359-11364 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T192 11382-11383 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T193 11499-11502 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T194 11514-11518 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T195 11616-11620 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T196 11711-11716 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T197 11743-11746 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T198 11796-11799 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T199 12177-12180 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T200 12181-12188 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T201 12240-12241 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 12283-12287 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T203 12291-12297 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T204 12361-12365 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T205 12477-12480 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T206 12502-12507 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T207 12606-12609 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T208 12626-12629 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T209 12660-12665 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T210 12684-12688 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T211 12699-12703 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T212 12705-12708 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T213 12725-12728 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T214 12859-12862 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T215 12974-12977 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T216 13199-13200 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 13409-13414 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T218 13607-13612 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T219 13712-13717 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T220 13732-13738 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T221 13974-13979 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T222 14061-14066 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T223 14083-14089 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T224 14091-14093 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T225 14099-14102 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T226 14269-14270 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T227 14276-14281 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T228 14454-14455 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T15 175-179 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T16 1162-1168 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T17 2021-2024 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T18 2128-2132 Chemical denotes UREA http://purl.obolibrary.org/obo/CHEBI_16199
T19 2223-2230 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T20 2249-2252 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T21 2255-2264 Chemical denotes aspartate http://purl.obolibrary.org/obo/CHEBI_132943|http://purl.obolibrary.org/obo/CHEBI_29995|http://purl.obolibrary.org/obo/CHEBI_72314
T24 2288-2296 Chemical denotes creatine http://purl.obolibrary.org/obo/CHEBI_16919|http://purl.obolibrary.org/obo/CHEBI_57947
T26 2313-2323 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T27 2352-2362 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T28 2364-2368 Chemical denotes UREA http://purl.obolibrary.org/obo/CHEBI_16199
T29 2371-2375 Chemical denotes Urea http://purl.obolibrary.org/obo/CHEBI_16199
T30 2376-2384 Chemical denotes nitrogen http://purl.obolibrary.org/obo/CHEBI_25555
T31 2391-2402 Chemical denotes haemoglobin http://purl.obolibrary.org/obo/CHEBI_35143
T32 2410-2417 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996
T33 6016-6026 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T34 6812-6822 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T35 7257-7259 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T36 7272-7274 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T38 7277-7279 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T39 7852-7854 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T40 7871-7873 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T42 7876-7878 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T43 9666-9676 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T44 9787-9797 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T45 9829-9831 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T46 9848-9850 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T47 10044-10051 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T48 10271-10273 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T49 10528-10535 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T50 10677-10682 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T51 10688-10692 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T52 10800-10802 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T53 11045-11055 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T54 11325-11335 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T55 11573-11583 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T56 11747-11749 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T57 11771-11781 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T58 11800-11802 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T59 11823-11833 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T60 12481-12483 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T61 12610-12612 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T62 12630-12632 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T63 12709-12711 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T64 12729-12731 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T65 12863-12865 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T66 12978-12980 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T67 13648-13657 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T7 84-93 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T8 227-232 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T9 263-268 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T10 433-438 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 440-446 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T12 448-453 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T13 790-809 Phenotype denotes pulmonary opacities http://purl.obolibrary.org/obo/HP_0031457
T14 1120-1139 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T15 1213-1229 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T16 1376-1395 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T17 2711-2720 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T18 2736-2745 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T19 3246-3255 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T20 3932-3941 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T21 4197-4206 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T22 13242-13251 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 883-899 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T3 2081-2086 http://purl.obolibrary.org/obo/GO_0004111 denotes CK-MB
T4 2305-2310 http://purl.obolibrary.org/obo/GO_0004111 denotes CK-MB

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T65 0-22 Sentence denotes Results and discussion
T66 23-146 Sentence denotes On 2nd January 2020, samples were collected from two unusual pneumonia patients from Zhongnan Hospital of Wuhan University.
T67 147-359 Sentence denotes Patient 1 was a 39-year-old male staff at Huanan Seafood Market who experienced fever (up to 37.7°C) and aggravated cough with frothy white sputum for 5 days before admitted to the hospital on 25th December 2019.
T68 360-570 Sentence denotes Patient 2 was a 21-year-old female who developed an intermittent febrile cough, chills, fever (up to 40°C), and frothy white sputum after having a contact with Huanan Seafood Market staff on 22nd December 2019.
T69 571-645 Sentence denotes She was admitted on 28th December after unsuccessful outpatient treatment.
T70 646-744 Sentence denotes The results of clinical laboratory test on the first day of hospitalization are listed in Table 1.
T71 745-924 Sentence denotes Chest CT scan of both patients showed patchy pulmonary opacities below the pleura in the bilateral lung field (Figure S1), which suggests viral infections may occur in both lungs.
T72 925-1030 Sentence denotes However, the subsequent routine anti-viral and anti-infection treatment did not alleviate their symptoms.
T73 1031-1180 Sentence denotes On 31st December 2019, patient 1 had more severe symptoms, including poor mental states, shortness of breath, and 86% SpO2 without oxygen inhalation.
T74 1181-1338 Sentence denotes A CT re-examination showed mild pleural effusion in the left lung, an increase in the density of ground-glass opacities, and an extension of the patchy area.
T75 1339-1412 Sentence denotes The patient later experienced Type I respiratory failure on the same day.
T76 1413-1528 Sentence denotes On 2nd January 2020, both patients were transferred to Wuhan Infectious Diseases Hospital for continuing treatment.
T77 1529-1707 Sentence denotes To the date this manuscript was prepared, patient 1 and patient 2 were later discharged from the hospital in stable condition on 12th January and 11th January 2020, respectively.
T78 1708-1716 Sentence denotes Table 1.
T79 1717-1778 Sentence denotes Clinical laboratory test on the first day of hospitalization.
T80 1779-1823 Sentence denotes Items Case 1 Case 2 Normal range of lab test
T81 1824-1853 Sentence denotes WBC, ×109/L 5.23 2.89 3.5–9.5
T82 1854-1893 Sentence denotes Neutrophils, ×109/L/L 3.58 1.92 1.8–6.3
T83 1894-1932 Sentence denotes T lymphocyte, ×109/L 1.32 0.46 1.1–3.2
T84 1933-1960 Sentence denotes Hb, g/L 138.6 127.5 115–150
T85 1961-1993 Sentence denotes Platelet, ×109/L 170 117 125–350
T86 1994-2020 Sentence denotes Albumin, g/L 65.9 47 40–55
T87 2021-2040 Sentence denotes AST, U/L 92 33 7–45
T88 2041-2061 Sentence denotes ALT, U/L 30 30 13–45
T89 2062-2080 Sentence denotes CK, U/L 36 35 <171
T90 2081-2102 Sentence denotes CK-MB, U/L 11 10 0–25
T91 2103-2127 Sentence denotes LDH, U/L 313 247 110–245
T92 2128-2158 Sentence denotes UREA, mmol/L 2.81 2.7 2.8–7.60
T93 2159-2187 Sentence denotes CREA, μmol/L 73.9 57.2 49–90
T94 2188-2457 Sentence denotes Definition of abbreviations: ALT = alanine aminotransferase; AST = aspartate aminotransferase; CK = creatine kinase; CK-MB = creatinine kinase–MB isoenzyme; CREA = creatinine; UREA = Urea nitrogen; Hb = haemoglobin; LDH = lactate dehydrogenase; WBC = white blood count.
T95 2458-2793 Sentence denotes On 3rd January 2020, respiratory and blood samples obtained from the patients were subjected to routine clinical laboratory tests for respiratory pathogens, including Influenza virus, Respiratory syncytial virus, Adenovirus, Metapneumovirus, Mycoplasma pneumonia, Chlamydophila pneumonia, and Legionella, all yielding negative results.
T96 2794-2923 Sentence denotes The remaining RNA samples were first subjected to SARS-CoV specific RT-PCR assays recommended by World Health Organization (WHO).
T97 2924-2983 Sentence denotes However, only one set yielded positive results (Figure 1A).
T98 2984-3161 Sentence denotes Further sequencing of the corresponding PCR product surprisingly suggested that the virus discovered is more closely related to BtCoV/4991 (97.35%) but not SARS-CoV (Figure 1B).
T99 3162-3171 Sentence denotes Figure 1.
T100 3172-3403 Sentence denotes 1st-round of RT-PCR assay, amplification and sequence analysis of unusual pneumonia outbreak in Wuhan. (A) RNA samples were subjected to SARS-CoV specific RT-PCR primer sets as indicated, only the SAR1-s/as set showed obvious band.
T101 3404-3451 Sentence denotes Lane 1, 6, 11, 16, 21 are samples of patient 1.
T102 3452-3499 Sentence denotes Lane 2, 7, 12, 17, 22 are samples of patient 2.
T103 3500-3632 Sentence denotes Other lanes are samples of other patients who are irrelevant to this study. (B) The Blast result of PCR products of patient 1 and 2.
T104 3633-3875 Sentence denotes On 4th January 2020, in 2nd-round RT-PCR assay, extended RdRp fragments and more genome fragments were identified, amplified, sequenced and analysed using new set of primers that were designed based on the 1st-round Blast analysis (Figure 2).
T105 3876-3982 Sentence denotes These data further suggest that the pathogen of unusual pneumonia might be a coronavirus but not SARS-CoV.
T106 3983-4147 Sentence denotes Meanwhile, total RNA extracted from BALF samples (collected on 2nd January 2020) were subject to metagenomic next-generation sequencing (mNGS) library construction.
T107 4148-4157 Sentence denotes Figure 2.
T108 4158-4296 Sentence denotes 2nd-round of identification of unusual pneumonia. (A) RNA samples were subjected to multiple primer sets for different genes as indicated.
T109 4297-4377 Sentence denotes Lane 1, 3, 5, 7, 9, 11, 12, 13, 14, 15, 21, 23, 25, 27 are samples of patient 1.
T110 4378-4544 Sentence denotes Lane 2, 4, 6, 8, 10, 16, 17, 18, 19, 20, 22, 24, 26, 28 are samples of patient 2. (B) The PCR product of patient 1 and 2 were sequenced and the Blast result is shown.
T111 4545-4610 Sentence denotes On 5th January 2020, the mNGS library construction was completed.
T112 4611-4731 Sentence denotes On 6th January 2020, the resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform.
T113 4732-4903 Sentence denotes On 7th January 2020, the sequencing results were obtained in less than 24 h, with 7,369,020 and 4,522,558 reads generated for the samples of patient 1 and 2, respectively.
T114 4904-5060 Sentence denotes To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline based on individual reads was carried out on sequenced data.
T115 5061-5239 Sentence denotes Aside from those belonged to PhiX genome (in-library control), a majority of the viral reads (99.9% and 99.7% respectively for sample 1 and 2) were associated with coronaviruses.
T116 5240-5382 Sentence denotes The raw sequence data minus human genomic information was uploaded to Sequence Read Archive (SRA) database (Bioproject accession PRJNA601736).
T117 5383-5639 Sentence denotes On the other hand, bacterial pathogen identification was carried out by using the Metaphlan2 program, which revealed Capnocytophaga sp and Veillonella sp in sample 2 and none in sample 1, and both bacteria identified were not known for their pathogenicity.
T118 5640-5731 Sentence denotes Collectively, coronavirus is likely to be the main microbial pathogen within these samples.
T119 5732-5834 Sentence denotes The reads were assembled de novo using Megahit to form a ∼30 kb contigs with sequence homology to CoV.
T120 5835-5908 Sentence denotes After confirmation with read mapping, the final CoV genome was 29,881 nt.
T121 5909-5994 Sentence denotes On 8th January 2020, the genome comparisons and evolutionary analyses were performed.
T122 5995-6225 Sentence denotes Although some single nucleotide polymorphism (SNP) profiles were identified in the mNGS data (Table 2), the consensus genome sequences obtained from the patient 1 and 2 were identical (GenBank MN988668 and MN988669, respectively).
T123 6226-6333 Sentence denotes These results indicated that these two individual patients were infected by the same CoV at separate times.
T124 6334-6450 Sentence denotes We named the two clinical isolates as 2019-nCoV strain WHU01 and WHU02, respectively, according to WHO announcement.
T125 6451-6796 Sentence denotes Based on the results of genome mapping, our data revealed extremely high viral abundance within the samples: the average genome coverage was 523.6X and 133.7X and the estimated abundance level were 1.5% and 0.62% of total reads sequenced for patient 1 and 2, respectively, suggesting active coronaviral replication in the lungs of both patients.
T126 6797-6805 Sentence denotes Table 2.
T127 6806-6871 Sentence denotes Minor nucleotide variant identified from WHU01 and WHU02 genomes.
T128 6872-6991 Sentence denotes Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value
T129 6992-7053 Sentence denotes WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07
T130 7054-7119 Sentence denotes WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14
T131 7120-7183 Sentence denotes WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27
T132 7184-7247 Sentence denotes WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14
T133 7248-7310 Sentence denotes WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13
T134 7311-7374 Sentence denotes WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14
T135 7375-7438 Sentence denotes WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29
T136 7439-7501 Sentence denotes WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10
T137 7502-7566 Sentence denotes WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10
T138 7567-7629 Sentence denotes WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08
T139 7630-7692 Sentence denotes WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07
T140 7693-7774 Sentence denotes WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20
T141 7775-7842 Sentence denotes WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14
T142 7843-7913 Sentence denotes WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10
T143 7914-7982 Sentence denotes WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13
T144 7983-8052 Sentence denotes WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23
T145 8053-8122 Sentence denotes WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47
T146 8123-8191 Sentence denotes WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09
T147 8192-8258 Sentence denotes WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28
T148 8259-8326 Sentence denotes WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07
T149 8327-8389 Sentence denotes WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0
T150 8390-8464 Sentence denotes WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08
T151 8465-8528 Sentence denotes WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56
T152 8529-8594 Sentence denotes WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51
T153 8595-8658 Sentence denotes WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41
T154 8659-8712 Sentence denotes WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16
T155 8713-8782 Sentence denotes WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32
T156 8783-8852 Sentence denotes WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31
T157 8853-8922 Sentence denotes WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138
T158 8923-8992 Sentence denotes WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57
T159 8993-9060 Sentence denotes WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50
T160 9061-9129 Sentence denotes WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57
T161 9130-9203 Sentence denotes WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10
T162 9204-9424 Sentence denotes Since 3rd January 2020, instant progress reports have been sent to the Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization.
T163 9425-9525 Sentence denotes The genomes of the 2019-nCoV were further analysed to determine its origin and evolutionary history.
T164 9526-9636 Sentence denotes Full genome comparisons indicated that 2019-nCoV is close to CoVs circulating in Rhinolophus (Horseshoe bats).
T165 9637-9963 Sentence denotes For example, it shared 98.7% nucleotide identity to bat coronavirus strain BtCoV/4991 (GenBank KP876546, only 370 nt sequence of RdRp gene) and 87.9% nucleotide identity to bat CoV strain bat-SL-CoVZC45 and bat-SL-CoVZXC21, indicating that it was quite divergent from the currently known human CoV, including SARS-CoV (79.7%).
T166 9964-10135 Sentence denotes To put 2019-nCoV in the context of whole Coronaviridae family, we aligned ORF1b protein sequences from representative CoVs diversity for phylogenetic analyses (Figure 3A).
T167 10136-10348 Sentence denotes It revealed that the 2019-nCoV is grouped under genus β-coronavirus, subgenus Sarbecovirus, and a cluster that is known to harbour bat-SL-CoVs, many of which were associated with Rhinolophus sp. (horseshoe bats).
T168 10349-10358 Sentence denotes Figure 3.
T169 10359-10416 Sentence denotes Origin and evolutionary history of newly identified CoVs.
T170 10417-10483 Sentence denotes A. the position of 2019-nCoV in the context of all reference CoVs.
T171 10484-10546 Sentence denotes The phylogeny is constructed based on ORF1b protein alignment.
T172 10547-10611 Sentence denotes For clarity, names were only shown for human-associated viruses.
T173 10612-10711 Sentence denotes Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively.
T174 10712-10876 Sentence denotes B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome.
T175 10877-10938 Sentence denotes Recombination breakpoints are shown as dashed vertical lines.
T176 10939-11004 Sentence denotes C. the relationship of WHU viruses with the other SARS-like CoVs.
T177 11005-11104 Sentence denotes Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N.
T178 11105-11213 Sentence denotes Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue.
T179 11214-11394 Sentence denotes To reveal a more detailed relationship between 2019-nCoV and other CoVs, we reconstructed phylogenies based on nucleotide alignment of key viral genes, including ORF1a/b, S, and N.
T180 11395-11503 Sentence denotes Within this cluster, the 2019-nCoV also shared close relationship with CoVs originated from Rhinolophus bat.
T181 11504-11880 Sentence denotes For ORF1b gene, the closest relative is BtCoV/4991 (KP876546, 98.65% nucleotide identity, based on partial RdRp gene comparisons) identified from Rhinolophus affinis from Yunnan; whereas for the rest of the genes analysed, the closest are bat-SL-CoVZXC21 (76.5–91.2% nucleotide identity) and bat-SL-CoVZC45 (76.9–91.2% nucleotide identity) identified from Rhinolophus sinicus.
T182 11881-11992 Sentence denotes The close relationship with BtCoV/4991 is quite essential in tracing the potential reservoir host of 2019-nCoV.
T183 11993-12127 Sentence denotes Unfortunately, the BtCoV/4991 sequence was only partial (373bp in length) and thus no comparisons can be made for the rest of genomes.
T184 12128-12352 Sentence denotes However, the presence of such close relatives in bat viruses strongly suggests that it might be originated from a recent and independent introduction from bats to humans, although its immediate hosts remain to be identified.
T185 12353-12550 Sentence denotes Through gene-specific phylogenetic analyses, we also identified phylogenetic incongruence for 2019-nCoV compared with other bat-SL-CoVs at different genes, suggesting potential recombination event.
T186 12551-12689 Sentence denotes Specifically, 2019-nCoV was closely related to strains bat-SL-CoVZXC21 and bat-SL-CoVZC45 at ORF1a, S, and N genes, but not at ORF1b gene.
T187 12690-12801 Sentence denotes At ORF1b gene, bat-SL-CoVZXC21 and bat-SL-CoVZC45 were related to strains Longquan-140 and HKU3-10 (Figure 2C).
T188 12802-13001 Sentence denotes Simplot analyses based on genome alignment of 2019-nCoV, bat-SL-CoVZC45, Longquan-140, and SARS-CoV suggest that the recombinant strain was not likely to be 2019-nCoV, but bat-SL-CoVZC45 (Figure 3B).
T189 13002-13164 Sentence denotes And it also revealed at least four recombination breakpoints at positions 11,754, 20,664, 22,321, and 24,134 nt of the genome alignment, respectively (Figure 3B).
T190 13165-13252 Sentence denotes In conclusion, we have identified a novel CoV from two patients with unusual pneumonia.
T191 13253-14318 Sentence denotes Although the direct association with the disease is yet to be confirmed with more experimental data, our results provide several lines of evidence that the virus is most likely associated with this disease: (i) the viral titre is very high, with the abundance level reaching 1.5% and 0.62% of total reads sequenced, surpassing the highest expressed host genes to be one of the most dominant RNA molecules in the host transcriptome, an important sign that the virus is then under active replication [9]; (ii) since our RNA mNGS approach targets the total infectome (except for prion) [10], the fact that no other pathogens were identified from the infected sample underlines the unique role played by 2019-nCoV; (iii) the virus is grouped within the notorious CoV clade (i.e. SARS-like) with history of cross-virus transmission to humans [11] and has been demonstrated to have strong zoonotic potential [12]; and while this manuscript was under preparation, we noticed another case report from Wuhan which identified a same virus as the one found in this study [13].
T192 14319-14514 Sentence denotes Collectively, these results use the rich information present in the RNA metagenomics to evaluate potential pathogens, which highlights a future trend of viral diagnosis in the age of information.

MyTest

Id Subject Object Predicate Lexical cue
32020836-30355154-27792009 13752-13753 30355154 denotes 9
32020836-29190287-27792010 14091-14093 29190287 denotes 11
32020836-26552008-27792011 14156-14158 26552008 denotes 12
32020836-31987001-27792012 14314-14316 31987001 denotes 13

2_test

Id Subject Object Predicate Lexical cue
32020836-30355154-27792009 13752-13753 30355154 denotes 9
32020836-29190287-27792010 14091-14093 29190287 denotes 11
32020836-26552008-27792011 14156-14158 26552008 denotes 12
32020836-31987001-27792012 14314-14316 31987001 denotes 13