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PMC:7029452 / 10267-17740 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
153 217-225 Disease denotes COVID-19 MESH:C000657245
162 1066-1070 Gene denotes RdRp Gene:43740578
163 257-264 Species denotes patient Tax:9606
164 409-414 Disease denotes fever MESH:D005334
165 416-425 Disease denotes headaches MESH:D006261
166 430-435 Disease denotes cough MESH:D003371
167 703-711 Disease denotes COVID-19 MESH:C000657245
168 846-866 Disease denotes SARS-CoV-2 infection MESH:C000657245
169 868-877 Disease denotes Infection MESH:D007239
171 1256-1264 Disease denotes COVID-19 MESH:C000657245
174 1321-1323 Gene denotes GP Gene:55819
175 1377-1396 Disease denotes infectious diseases MESH:D003141
178 1402-1409 Species denotes patient Tax:9606
179 1525-1532 Species denotes persons Tax:9606
194 2467-2471 Gene denotes RdRp Gene:43740578
195 2383-2396 Gene denotes Cases 2 and 3
196 2533-2537 Gene denotes RdRp Gene:43740578
197 2284-2294 Species denotes SARS-CoV-2 Tax:2697049
198 2488-2497 Species denotes 2019-nCov Tax:2697049
199 1816-1821 Disease denotes fever MESH:D005334
200 1831-1838 Disease denotes fatigue MESH:D005221
201 1840-1854 Disease denotes conjunctivitis MESH:D003231
202 1859-1864 Disease denotes cough MESH:D003371
203 1969-1974 Disease denotes fever MESH:D005334
204 1984-1991 Disease denotes fatigue MESH:D005221
205 1996-2001 Disease denotes cough MESH:D003371
206 2259-2267 Disease denotes COVID-19 MESH:C000657245
207 2269-2278 Disease denotes Infection MESH:D007239
211 2651-2658 Species denotes patient Tax:9606
212 2796-2802 Chemical denotes oxygen MESH:D010100
213 2839-2858 Disease denotes infectious diseases MESH:D003141
215 2981-2988 Species denotes persons Tax:9606
218 3212-3225 Gene denotes Cases 2 and 3
219 3205-3210 Disease denotes cough MESH:D003371
223 3710-3713 Gene denotes SpF Gene:23541
224 3336-3346 Species denotes SARS-CoV-2 Tax:2697049
225 3321-3330 Disease denotes infection MESH:D007239
227 3788-3821 Gene denotes Early Warning and Response System
235 4239-4246 Species denotes patient Tax:9606
236 4592-4599 Species denotes persons Tax:9606
237 5501-5508 Species denotes patient Tax:9606
238 4099-4108 Disease denotes infection MESH:D007239
239 4390-4399 Disease denotes infection MESH:D007239
240 4497-4505 Disease denotes coughing MESH:D003371
241 5263-5272 Disease denotes infection MESH:D007239
248 5608-5621 Gene denotes Cases 2 and 3
249 6039-6044 Species denotes child Tax:9606
250 6441-6449 Species denotes patients Tax:9606
251 5833-5842 Disease denotes infection MESH:D007239
252 6133-6142 Disease denotes infection MESH:D007239
253 6220-6229 Disease denotes infection MESH:D007239
262 7058-7071 Gene denotes Cases 2 and 3
263 6973-6983 Species denotes SARS-CoV-2 Tax:2697049
264 7313-7323 Species denotes SARS-CoV-2 Tax:2697049
265 6519-6527 Disease denotes COVID-19 MESH:C000657245
266 6806-6826 Disease denotes respiratory symptoms MESH:D012818
267 6958-6967 Disease denotes Infection MESH:D007239
268 7082-7102 Disease denotes respiratory symptoms MESH:D012818
269 7298-7307 Disease denotes Infection MESH:D007239
271 7464-7472 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T8 460-464 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T9 987-991 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T10 1157-1161 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 2612-2616 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T12 2831-2835 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T13 5357-5361 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T14 5365-5369 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T15 6329-6333 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T16 6337-6341 Body_part denotes face http://purl.org/sig/ont/fma/fma24728

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 5357-5361 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T9 5365-5369 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T10 6329-6333 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T11 6337-6341 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T57 217-225 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T58 374-376 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T59 683-685 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T60 703-711 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T61 846-854 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 846-850 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 857-866 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T64 868-877 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T65 1256-1264 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T66 1377-1387 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T67 1840-1854 Disease denotes conjunctivitis http://purl.obolibrary.org/obo/MONDO_0003799
T68 2259-2267 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T69 2269-2278 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T70 2284-2292 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 2284-2288 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 2690-2692 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T73 2839-2849 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T74 3321-3330 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T75 3336-3344 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 3336-3340 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T77 4099-4108 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T78 4390-4399 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 5263-5272 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T80 5833-5842 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T81 6133-6142 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T82 6220-6229 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 6519-6527 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T84 6958-6967 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T85 6973-6981 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 6973-6977 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T87 7298-7307 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T88 7313-7321 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T89 7313-7317 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T90 7464-7472 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T74 238-239 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 240-242 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T76 252-256 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T77 252-256 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T78 488-490 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T79 579-580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 639-640 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 956-962 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T82 987-991 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T83 1157-1161 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T84 1496-1503 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T85 1635-1636 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 1699-1700 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 1721-1725 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T88 1721-1725 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T89 1756-1758 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T90 1891-1892 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 1913-1919 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T92 2176-2177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T93 2472-2475 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes Pan
T94 2506-2510 http://purl.obolibrary.org/obo/CLO_0037161 denotes E; N
T95 2612-2616 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T96 2646-2650 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T97 2646-2650 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T98 2952-2959 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T99 3043-3044 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 3192-3193 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 3446-3447 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 4794-4795 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 5357-5361 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T104 5365-5369 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T105 5658-5668 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T106 5901-5902 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 5955-5956 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 6005-6007 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T109 6329-6333 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T110 6337-6341 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T111 6660-6661 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T112 6766-6767 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 6830-6832 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T114 6863-6864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 7014-7015 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T116 7139-7140 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 7440-7443 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 252-256 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T6 1071-1073 Chemical denotes IP http://purl.obolibrary.org/obo/CHEBI_74076
T7 1295-1297 Chemical denotes ED http://purl.obolibrary.org/obo/CHEBI_73503
T8 1321-1323 Chemical denotes GP http://purl.obolibrary.org/obo/CHEBI_70744
T9 1373-1375 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T10 1721-1725 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T11 2538-2540 Chemical denotes IP http://purl.obolibrary.org/obo/CHEBI_74076
T12 2646-2650 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T13 2796-2802 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T10 409-414 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T11 416-425 Phenotype denotes headaches http://purl.obolibrary.org/obo/HP_0002315
T12 430-435 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T13 1816-1821 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T14 1823-1829 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T15 1831-1838 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T16 1840-1854 Phenotype denotes conjunctivitis http://purl.obolibrary.org/obo/HP_0000509
T17 1859-1864 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T18 1969-1974 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T19 1976-1982 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T20 1984-1991 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T21 1996-2001 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T22 3205-3210 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T23 4497-4505 Phenotype denotes coughing http://purl.obolibrary.org/obo/HP_0012735

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 4818-4824 http://purl.obolibrary.org/obo/GO_0060361 denotes flight
T4 5083-5089 http://purl.obolibrary.org/obo/GO_0060361 denotes flight
T5 6730-6736 http://purl.obolibrary.org/obo/GO_0060361 denotes flight

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T69 0-7 Sentence denotes Results
T70 9-33 Sentence denotes Detected confirmed cases
T71 34-226 Sentence denotes Between 10 January and 24 January (period until confirmation of the first cases in France), nine possible cases were identified in France; among them, three cases were confirmed with COVID-19.
T72 227-282 Sentence denotes Case 1 was a 48-year-old male patient living in France.
T73 283-451 Sentence denotes He was travelling for professional reasons in China in various cities including Wuhan when he experienced his first symptoms (fever, headaches and cough) on 16 January.
T74 452-558 Sentence denotes He flew back to Bordeaux, France on 22 January via Shanghai, Qingdao and Paris Charles de Gaulle airports.
T75 559-605 Sentence denotes He reported wearing a mask during the flights.
T76 606-867 Sentence denotes He sought medical attention from a general practitioner on 23 January, where he was suspected of COVID-19, and was subsequently transferred to the regional referring hospital in Bordeaux, isolated and sampled for laboratory confirmation of SARS-CoV-2 infection.
T77 868-948 Sentence denotes Infection was confirmed on 24 January by the National Reference Centre (Figure).
T78 949-1169 Sentence denotes Case 1 tested positive only for the E gene target when using the Charité procedure [4] and was positive for all four RdRp-IP targets with threshold cycles (Ct) in good agreement with those obtained for the E gene target.
T79 1170-1294 Sentence denotes Figure Timeline of travel, onset of illness and close contacts of confirmed cases of COVID-19, France, January 2020 (n = 3)
T80 1295-1397 Sentence denotes ED: emergency department; GP: general practitioner; ICU: intensive care unit; ID: infectious diseases.
T81 1398-1549 Sentence denotes The patient arrived in Wuhan on 13 January, did not report any visit to markets, exposure to live animals or contact with sick persons during his stay.
T82 1550-1687 Sentence denotes No detailed information is available about the circumstances of exposure, apart from a visit to family members and friends on 15 January.
T83 1688-1802 Sentence denotes Case 2 was a 31-year-old Chinese male tourist who had left Wuhan on 18 January and arrived in Paris on 19 January.
T84 1803-1879 Sentence denotes He developed fever, chills, fatigue, conjunctivitis and cough on 19 January.
T85 1880-1954 Sentence denotes Case 3 was a 30-year-old Chinese female tourist who travelled with Case 2.
T86 1955-2016 Sentence denotes She developed fever, chills, fatigue and cough on 23 January.
T87 2017-2268 Sentence denotes On 24 January, they were advised by the Chinese embassy to seek medical attention at the national hotline (SAMU-centre 15) and were immediately transferred to a regional referring hospital, isolated and sampled for laboratory confirmation of COVID-19.
T88 2269-2382 Sentence denotes Infection with SARS-CoV-2 was confirmed on 24 January for both of them by the National Reference Centre (Figure).
T89 2383-2624 Sentence denotes Cases 2 and 3 were positive by RT-PCR for all targets of the Charité procedure [4] (RdRp Pan Sarbeco and 2019-nCov probes; E; N) as well for the four RdRp-IP targets with Ct values in good agreement with those obtained for the E gene target.
T90 2625-2752 Sentence denotes The condition of the male patient deteriorated on 29 January and he was admitted to the intensive care unit (ICU) the same day.
T91 2753-2878 Sentence denotes He stayed 72 h in the ICU for non-invasive oxygen therapy and was transferred back to infectious diseases ward on 31 January.
T92 2879-3029 Sentence denotes Neither of the two cases reported any visit to markets, exposure to live animals or contact with sick persons during the 14 days before symptom onset.
T93 3030-3131 Sentence denotes Both visited a hospital in Wuhan on 16 January for an unrelated medical condition in Case 3 (Figure).
T94 3132-3211 Sentence denotes As at 12 February, Case 1 was afebrile and symptomatic with a persistent cough.
T95 3212-3305 Sentence denotes Cases 2 and 3 were not symptomatic any more and were discharged from hospital on 12 February.
T96 3306-3533 Sentence denotes As soon as the infection with SARS-CoV-2 was confirmed for the three cases on 24 January, this information was immediately released through a press conference held by the French Minister of Health and the Chief Medical Officer.
T97 3534-3668 Sentence denotes Daily public communication on the state of the investigations around the cases was subsequently implemented by the Ministry of Health.
T98 3669-3722 Sentence denotes Daily updates were also published on the SpF website.
T99 3723-3972 Sentence denotes The three cases were notified to the European Commission via the Early Warning and Response System (EWRS) on 26 January, and to the European Center for Disease Prevention and Control (ECDC) via the European Surveillance System (TESSy) on 28 January.
T100 3974-4007 Sentence denotes Contact and co-exposition tracing
T101 4008-4055 Sentence denotes No co-exposed person was identified for Case 1.
T102 4056-4330 Sentence denotes Two contacts were evaluated at low risk of infection, the taxi driver who drove the case from the airport to his home (30-min drive) and the general practitioner who took care of the patient before wearing appropriate personal protection equipment (3-min non-close contact).
T103 4331-4400 Sentence denotes Seventeen contacts were evaluated at moderate/high risk of infection.
T104 4401-4560 Sentence denotes Four of them shared the same waiting room in the general practitioner’s office while Case 1 was coughing, seated ca 1–1.5 m away from the case during 5–30 min.
T105 4561-4697 Sentence denotes The other 13 contacts were the persons sitting in the two seats around Case 1 in the Shanghai–Paris and Paris–Bordeaux flights (Figure).
T106 4698-5039 Sentence denotes They were considered at moderate risk of exposure despite the fact that Case 1 reported wearing a mask during the whole flight; this was based on the length of one of the flights (> 6 h) and the fact that it was unclear whether or not Case 1 removed his mask during short periods (e.g. meals) and kept the same mask during the whole flights.
T107 5040-5195 Sentence denotes None of the contacts of the Shanghai–Paris flight were French nationals and their contact tracing was referred to their home countries’ health authorities.
T108 5196-5607 Sentence denotes All other identified contacts were evaluated at negligible risk of infection because the contacts were short and/or distant in public settings and did not imply face-to-face conversations or because appropriate personal protective equipment (PPE) was worn by the healthcare personnel who took care of the patient, including those involved in the transfer from the general practitioner to the referring hospital.
T109 5608-5787 Sentence denotes Cases 2 and 3 stayed together and shared the same activities during their stay in Paris, and therefore shared the same contacts from 23 January (date of illness onset for Case 3).
T110 5788-6016 Sentence denotes Three contacts were evaluated at low risk of infection: the two owners of the apartment rented by the couple and a department store employee with whom Case 2 reported a distant (> 1 m) contact during around 20 min on 22 January.
T111 6017-6152 Sentence denotes The apartment owner’s child who visited Cases 2 and 3 and was hugged by them was evaluated at moderate/high risk of infection (Figure).
T112 6153-6450 Sentence denotes All other identified contacts were evaluated at negligible risk of infection, as contacts were short and distant in public settings such as department stores and did not imply face-to-face conversations or because appropriate PPE was worn by the healthcare personnel who took care of the patients.
T113 6451-6546 Sentence denotes Follow-up of the identified contacts was initiated according to the COVID-19 procedure (Table).
T114 6547-6659 Sentence denotes As at 2 February, two contacts have been classified as possible cases since the implementation of the follow-up:
T115 6660-6957 Sentence denotes A person sitting two seats away from Case 1 during the Paris–Bordeaux flight, and therefore identified as a moderate/high risk contact, developed respiratory symptoms on 27 January and was classified as a possible case on 31 January and was subsequently excluded following negative RT-PCR results.
T116 6958-7013 Sentence denotes Infection with SARS-CoV-2 was excluded on the same day.
T117 7014-7169 Sentence denotes A radiology assistant who took care of both Cases 2 and 3 developed respiratory symptoms on 30 January and was classified as a possible case on 2 February.
T118 7170-7297 Sentence denotes This person had been classified as at negligible risk of exposure, because she wore appropriate PPE during the whole procedure.
T119 7298-7351 Sentence denotes Infection with SARS-CoV-2 was excluded on 2 February.
T120 7352-7398 Sentence denotes Follow-up of the contacts ended on 6 February.
T121 7399-7473 Sentence denotes No identified contact of the three cases has been confirmed with COVID-19.