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PMC:7029452 / 17742-25251 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
280 132-142 Species denotes SARS-CoV-2 Tax:2697049
281 907-911 Species denotes H1N1 Tax:114727
282 20-28 Disease denotes COVID-19 MESH:C000657245
283 187-195 Disease denotes COVID-19 MESH:C000657245
284 429-448 Disease denotes infectious diseases MESH:D003141
285 810-820 Disease denotes infections MESH:D007239
286 889-893 Disease denotes MERS MESH:D018352
287 919-937 Disease denotes Ebolavirus disease MESH:D019142
297 1610-1618 Species denotes SARS-CoV Tax:694009
298 1623-1631 Species denotes MERS-CoV Tax:1335626
299 1253-1284 Disease denotes lower acute respiratory disease MESH:D012120
300 1427-1447 Disease denotes respiratory symptoms MESH:D012818
301 1591-1599 Disease denotes COVID-19 MESH:C000657245
302 1761-1780 Disease denotes infectious diseases MESH:D003141
303 1962-1970 Disease denotes COVID-19 MESH:C000657245
304 2131-2162 Disease denotes lower acute respiratory disease MESH:D012120
305 2362-2370 Disease denotes COVID-19 MESH:C000657245
307 2893-2901 Disease denotes COVID-19 MESH:C000657245
311 3341-3348 Species denotes persons Tax:9606
312 3860-3867 Species denotes persons Tax:9606
313 3673-3692 Disease denotes infectious diseases MESH:D003141
318 3964-3974 Species denotes SARS-CoV-2 Tax:2697049
319 3997-4002 Species denotes human Tax:9606
320 4006-4011 Species denotes human Tax:9606
321 4871-4876 Disease denotes cough MESH:D003371
323 5027-5037 Species denotes SARS-CoV-2 Tax:2697049
326 5336-5346 Species denotes SARS-CoV-2 Tax:2697049
327 5437-5446 Disease denotes infection MESH:D007239
332 5713-5718 Species denotes human Tax:9606
333 5722-5727 Species denotes human Tax:9606
334 5552-5560 Disease denotes COVID-19 MESH:C000657245
335 6066-6074 Disease denotes COVID-19 MESH:C000657245
341 6439-6444 Species denotes human Tax:9606
342 6448-6453 Species denotes human Tax:9606
343 6470-6480 Species denotes SARS-CoV-2 Tax:2697049
344 6733-6743 Species denotes SARS-CoV-2 Tax:2697049
345 6137-6145 Disease denotes COVID-19 MESH:C000657245
348 7395-7405 Species denotes SARS-CoV-2 Tax:2697049
349 7172-7180 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T17 3755-3759 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T18 4547-4551 Body_part denotes back http://purl.org/sig/ont/fma/fma25056

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T12 2380-2389 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106
T13 3755-3759 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T91 20-28 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T92 132-140 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 132-136 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T94 187-195 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T95 429-439 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T96 810-820 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T97 847-880 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T98 882-886 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T99 895-912 Disease denotes influenza A(H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T100 895-904 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T101 919-937 Disease denotes Ebolavirus disease http://purl.obolibrary.org/obo/MONDO_0005737
T102 1265-1284 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T103 1591-1599 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 1610-1618 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 1610-1614 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T106 1761-1771 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T107 1962-1970 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 2143-2162 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T109 2362-2370 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T110 2893-2901 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T111 3673-3683 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T112 3964-3972 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T113 3964-3968 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T114 5027-5035 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T115 5027-5031 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T116 5336-5344 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T117 5336-5340 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T118 5437-5446 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T119 5552-5560 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T120 6066-6074 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T121 6137-6145 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T122 6470-6478 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T123 6470-6474 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T124 6733-6741 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T125 6733-6737 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T126 7172-7180 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T127 7395-7403 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T128 7395-7399 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T118 42-45 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T119 542-545 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T120 553-554 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 905-906 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T122 1071-1072 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1171-1183 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T124 1244-1245 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T125 1741-1742 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 3753-3754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 3755-3759 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T128 3997-4005 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human to
T129 4006-4011 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T130 4038-4039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 4122-4123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 5501-5507 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T133 5713-5718 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T134 5722-5727 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T135 5815-5820 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T136 6322-6331 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T137 6439-6444 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T138 6448-6453 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T139 6989-6999 http://purl.obolibrary.org/obo/BFO_0000030 denotes objectives
T140 7309-7312 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T141 7342-7348 http://purl.obolibrary.org/obo/CLO_0001658 denotes active

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T24 4871-4876 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T6 6503-6515 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T122 0-10 Sentence denotes Discussion
T123 11-152 Sentence denotes Specific COVID-19 surveillance has been in place in France since 10 January 2020, 3 days after the identification of the SARS-CoV-2 in China.
T124 153-277 Sentence denotes The first three imported cases of COVID-19 in France, the first ones in Europe, were diagnosed 14 days later, on 24 January.
T125 278-696 Sentence denotes Rapid and effective collaboration between the clinicians (general practitioners attending the cases, emergency hotline clinicians (SAMU-centre 15) and infectious diseases specialists), the National Reference Centre and the regional and national health authorities has played a crucial role in the system’s capacity to quickly detect, isolate and investigate those cases in order to implement adequate control measures.
T126 697-1047 Sentence denotes The surveillance system as well as the control measures were adapted from those implemented during past emerging infections that occurred after 2003 (severe acute respiratory syndrome (SARS), MERS, influenza A(H1N1)pdm09, Ebolavirus disease), and all involved parties were already familiar with the system, which probably favoured its responsiveness.
T127 1048-1285 Sentence denotes The case definition of a possible case in use on 24 January was slightly adapted from the one provided by the World Health Organization (WHO), based on an epidemiological link to Wuhan, China and a severe lower acute respiratory disease.
T128 1286-1498 Sentence denotes It is noteworthy that the first nine possible cases identified in France, including the three confirmed cases described here, displayed mild respiratory symptoms with no sign of severity at the time of diagnosis.
T129 1499-1636 Sentence denotes Increasing evidence suggests that mild clinical symptoms could be more frequent in cases of COVID-19 than with SARS-CoV and MERS-CoV [5].
T130 1637-1711 Sentence denotes Therefore, the case definition in effect on 24 January lacked sensitivity.
T131 1712-1924 Sentence denotes This was counter-balanced by a tendency from the infectious diseases specialists in charge of classification of suspected cases to privilege the exposure to Wuhan over the clinical presentation in their decision.
T132 1925-2065 Sentence denotes However, we cannot exclude that some COVID-19 cases remained undetected in France because of the lack of sensitivity of our case definition.
T133 2066-2232 Sentence denotes The clinical criteria were expanded on 4 February to include any lower acute respiratory disease and the epidemiological criterion was extended to the whole of China.
T134 2233-2371 Sentence denotes At that time, the French laboratory capacities were reinforced from one to five laboratories able to perform the diagnostics for COVID-19.
T135 2372-2474 Sentence denotes Further extension to all 38 referring hospital laboratories is expected by early to mid-February 2020.
T136 2475-2700 Sentence denotes Santé publique France will deploy in early February the outbreak investigation tool developed by the WHO (Go.Data [6]) in order to facilitate case data management and contact tracing at the national and local level in France.
T137 2701-2902 Sentence denotes Contact and co-exposure identification of the three confirmed cases had been initiated as soon as they were classified as possible cases, which facilitated investigations upon confirmation of COVID-19.
T138 2903-3152 Sentence denotes Confirmation of the diagnosis was made in the evening of 24 January and the investigation to retrieve as exhaustively as possible contacts and co-exposed individuals and evaluate their level of risk of transmission was started immediately overnight.
T139 3153-3279 Sentence denotes Complete transparency of the investigations was ensured through daily press conferences held by the French health authorities.
T140 3280-3521 Sentence denotes Although the follow-up procedure for the contacts/co-exposed persons used in France slightly differ from the ECDC and WHO guidelines [7,8], which were not available at the time of this investigation, it relies on the same general principles.
T141 3522-3721 Sentence denotes Contact tracing of the passengers seated near Case 1 during the two flights Shanghai–Paris and Paris–Bordeaux was adapted from the ECDC guidelines for infectious diseases transmitted on aircraft [9].
T142 3722-3904 Sentence denotes Even though Case 1 was wearing a face mask during those flights, we could not exclude breaches and subsequent risk of transmission to the persons sitting in the two seats around him.
T143 3905-4192 Sentence denotes Because of the current uncertainties about the capacity of SARS-CoV-2 to easily spread from human to human, the decision to consider a contact as close if the case–contact distance was between 1 m and 2 m was made on a case-by-case basis, depending on the type and length of interaction.
T144 4193-4385 Sentence denotes Through the extensive interviews made with the cases and their high compliance to cooperate to the investigation, we believe that the contacts most at risk have been satisfactorily identified.
T145 4386-4491 Sentence denotes All of them could be rapidly contacted and informed about measures to be taken, which they all agreed to.
T146 4492-4910 Sentence denotes However, some contacts were either impossible to trace back (e.g. co-travellers on public transportation) or evaluated as at negligible risk of exposure because of short and/or distant contacts (e.g. restaurant, contacts with cashiers while running errands, visiting museums), although accidental events carrying the risk of transmission on such occasions, such as an episode of cough of sneezing, cannot be ruled out.
T147 4911-4990 Sentence denotes Moreover, the contact tracing was limited to the period after onset of illness.
T148 4991-5215 Sentence denotes However, should the transmission of SARS-CoV-2 occur during the asymptomatic phase, we cannot exclude that secondary transmission events initiated from the three confirmed cases remained undetected during the investigations.
T149 5216-5310 Sentence denotes Case 3 developed symptoms 4 days after her husband and 5 days after the couple had left Wuhan.
T150 5311-5399 Sentence denotes The incubation period of SARS-CoV-2 is currently estimated at around 3–7 days [5,10,11].
T151 5400-5496 Sentence denotes Therefore, she may have acquired the infection from her husband, although this cannot be proved.
T152 5497-5847 Sentence denotes The active surveillance of close contacts of confirmed COVID-19 cases and the implementation of control measures, including home quarantine for those evaluated at moderate/high risk of exposure, decrease the risk of human-to-human transmission originating from imported cases and subsequently delay propagation of the virus in the general population.
T153 5848-5932 Sentence denotes This allows our healthcare system to prepare for any further spread of the epidemic.
T154 5933-6075 Sentence denotes Besides, the epidemiological and clinical data collected about the confirmed cases and their contacts will increase our knowledge of COVID-19.
T155 6076-6284 Sentence denotes The rapid and collaborative management of the first imported COVID-19 cases in France highlights the fact that the French healthcare system is adequately prepared to respond to such emerging diseases threats.
T156 6285-6382 Sentence denotes However, this surveillance system is extremely time-consuming and requires considerable manpower.
T157 6383-6553 Sentence denotes The data available on 12 February strongly suggest that human-to-human transmission of SARS-CoV-2 is frequent, with the reproduction number estimated at 2 to 3 [5,10-14].
T158 6554-6699 Sentence denotes Twenty-five countries have already reported imported cases from China, and several of them have described autochthonous transmission events [15].
T159 6700-6841 Sentence denotes In the case of further spread of SARS-CoV-2 worldwide, it would soon become impossible to detect all imported cases and trace their contacts.
T160 6842-6971 Sentence denotes Especially the occurrence of large clusters in the same region would strongly impact on the local health authorities’ capacities.
T161 6972-7101 Sentence denotes The surveillance objectives would then need to evolve from containing the epidemic to mitigating its medical and societal impact.
T162 7102-7276 Sentence denotes As at 12 February, the contacts of the three first confirmed cases of COVID-19 in France have been followed up for the whole 14 days follow-up time after the cases isolation.
T163 7277-7359 Sentence denotes No secondary transmission event has been detected so far despite active follow-up.
T164 7360-7509 Sentence denotes Given the first estimations of the SARS-CoV-2 incubation period, the probability of secondary cases originating from those three cases is negligible.