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PMC:7269710 / 3778-9246 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
63 122-128 Species denotes people Tax:9606
64 355-363 Species denotes patients Tax:9606
65 392-398 Species denotes people Tax:9606
66 430-436 Species denotes people Tax:9606
67 596-604 Species denotes patients Tax:9606
68 771-781 Species denotes SARS-CoV-2 Tax:2697049
69 149-157 Disease denotes COVID-19 MESH:C000657245
70 247-255 Disease denotes COVID-19 MESH:C000657245
71 340-348 Disease denotes COVID-19 MESH:C000657245
72 442-451 Disease denotes pneumonia MESH:D011014
73 695-703 Disease denotes COVID-19 MESH:C000657245
79 1230-1277 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
80 1279-1289 Species denotes SARS-CoV-2 Tax:2697049
81 1096-1104 Disease denotes COVID-19 MESH:C000657245
82 1141-1165 Disease denotes coronavirus disease 2019 MESH:C000657245
83 1167-1175 Disease denotes COVID-19 MESH:C000657245
87 1503-1513 Species denotes SARS-CoV-2 Tax:2697049
88 1626-1636 Species denotes SARS-CoV-2 Tax:2697049
89 1399-1407 Disease denotes COVID-19 MESH:C000657245
93 1965-1971 Species denotes people Tax:9606
94 1860-1868 Disease denotes COVID-19 MESH:C000657245
95 1919-1928 Disease denotes pneumonia MESH:D011014
98 2303-2311 Disease denotes COVID-19 MESH:C000657245
99 2460-2479 Disease denotes Infectious Diseases MESH:D003141
105 2598-2604 Species denotes people Tax:9606
106 2846-2852 Species denotes people Tax:9606
107 2981-2987 Species denotes people Tax:9606
108 2620-2628 Disease denotes COVID-19 MESH:C000657245
109 3003-3011 Disease denotes COVID-19 MESH:C000657245
112 3751-3757 Species denotes people Tax:9606
113 3635-3643 Disease denotes COVID-19 MESH:C000657245
120 4454-4472 Gene denotes C-reactive protein Gene:1401
121 4260-4266 Species denotes people Tax:9606
122 4549-4557 Species denotes patients Tax:9606
123 4566-4575 Chemical denotes lopinavir MESH:D061466
124 4590-4599 Chemical denotes ritonavir MESH:D019438
125 4282-4290 Disease denotes COVID-19 MESH:C000657245
128 4946-4955 Disease denotes infection MESH:D007239
129 5176-5184 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 159-167 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T2 818-826 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T3 4352-4357 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T4 4394-4399 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T5 4417-4422 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T6 4465-4472 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 4352-4357 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T2 4394-4399 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T3 4417-4422 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T28 149-157 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 340-348 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 442-451 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T31 487-496 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T32 695-703 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 771-779 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 1096-1104 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T35 1141-1165 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T36 1167-1175 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 1230-1277 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T38 1230-1263 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T39 1279-1287 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 1399-1407 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 1503-1511 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 1626-1634 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 1860-1868 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 1919-1928 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T45 1932-1941 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T46 2303-2311 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 2460-2470 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T48 2620-2628 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 3003-3011 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 3635-3643 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 4282-4290 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 4946-4955 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T53 5176-5184 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T17 77-80 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 168-171 http://purl.obolibrary.org/obo/CLO_0008337 denotes p 4
T19 331-335 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T20 591-595 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T21 675-676 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 737-738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 789-790 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 812-816 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T25 827-830 http://purl.obolibrary.org/obo/CLO_0008285 denotes p 1
T26 827-830 http://purl.obolibrary.org/obo/CLO_0008286 denotes p 1
T27 1121-1122 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 1291-1294 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T29 1794-1799 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T30 2073-2079 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T31 2700-2708 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T32 2863-2864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 2894-2895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3416-3424 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T35 3849-3859 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing as
T36 3868-3874 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T37 3958-3959 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 4028-4029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 4050-4056 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T40 4182-4183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 4352-4357 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T42 4352-4357 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T43 4383-4384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 4394-4399 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T45 4394-4399 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T46 4417-4422 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T47 4417-4422 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T48 4432-4437 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 4465-4472 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T6 4477-4484 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996
T7 4566-4575 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T8 4590-4599 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T34 0-7 Sentence denotes Methods
T35 9-21 Sentence denotes Study design
T36 22-173 Sentence denotes Since Jan 2, 2020, the Ministry of Health in Singapore has been refining local case-definitions for people suspected of having COVID-19 (appendix p 4).
T37 174-543 Sentence denotes Doctors are required by law to notify the Ministry of Health of cases of COVID-19.7 Further, Singapore implemented enhanced surveillance on Jan 31, 2020, to test for COVID-19 among patients in intensive care units and people who died of unknown cause, all people with pneumonia in hospitals, and individuals with influenza-like illness in sentinel primary-care clinics.
T38 544-674 Sentence denotes Hospital-based doctors also have permission to test patients who they view with suspicion for clinical or epidemiological reasons.
T39 675-832 Sentence denotes A confirmed case of COVID-19 is defined as an individual with a respiratory sample positive for SARS-CoV-2, using a laboratory-based PCR test (appendix p 1).
T40 833-932 Sentence denotes Phylogenetic analysis is done of available viral genomic sequences to ascertain genetic clustering.
T41 933-952 Sentence denotes Research in context
T42 953-979 Sentence denotes Evidence before this study
T43 980-1120 Sentence denotes We searched PubMed up to Feb 15, 2020 for reports published in English with no date limitations using the keywords “COVID-19” and “cluster”.
T44 1121-1213 Sentence denotes A family cluster of coronavirus disease 2019 (COVID-19) was reported in Shenzhen, Guangdong.
T45 1214-1342 Sentence denotes Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has also been reported among co-workers in Germany.
T46 1343-1368 Sentence denotes Added value of this study
T47 1369-1479 Sentence denotes We analysed three clusters of COVID-19 in Singapore to assess interactions and possible modes of transmission.
T48 1480-1579 Sentence denotes Our findings show that SARS-CoV-2 is transmissible in community settings beyond household clusters.
T49 1580-1733 Sentence denotes Importation and limited local transmission of SARS-CoV-2 could have occurred before the lockdown of Wuhan and China's institution of travel restrictions.
T50 1734-1776 Sentence denotes Implications of all the available evidence
T51 1777-2031 Sentence denotes Countries should focus on enhancing detection and containment of local clusters of COVID-19, through surveillance of individuals with general pneumonia or influenza-like illnesses, and of people who have been in contact with unwell travellers from China.
T52 2032-2227 Sentence denotes It is also important for countries to do active case-finding among close contacts of affected individuals, including contacts with mild symptoms, to contain clusters and stop them from spreading.
T53 2228-2363 Sentence denotes The Ministry of Health in Singapore identified the first three clusters of COVID-19 cases on Feb 3, 2020, Feb 5, 2020, and Feb 8, 2020.
T54 2364-2551 Sentence denotes All epidemiological investigations and outbreak containment measures were implemented under the Infectious Diseases Act,7 which provides for use of data for analysis to control outbreaks.
T55 2553-2582 Sentence denotes Epidemiological investigation
T56 2583-2784 Sentence denotes We interviewed people with confirmed COVID-19 to obtain data for demographic characteristics, clinical symptoms, and activity patterns, from 14 days preceding symptom onset until isolation in hospital.
T57 2785-2971 Sentence denotes We initiated contact tracing to identify close contacts (ie, people who spend a prolonged time within 2 m of a confirmed case) and other contacts who had some interactions with the case.
T58 2972-3110 Sentence denotes We asked people with confirmed COVID-19 about possible contact with confirmed cases reported overseas in the 14 days before symptom onset.
T59 3111-3309 Sentence denotes We used open source information from other countries (including government websites), news aggregators (eg, ProMed), and media reports to identify secondary transmissions in the respective clusters.
T60 3310-3403 Sentence denotes For each cluster, we investigated the implicated setting to ascertain potential interactions.
T61 3404-3528 Sentence denotes We reviewed activity maps of other confirmed cases in Singapore to identify potential epidemiological links to each cluster.
T62 3529-3710 Sentence denotes We placed close contacts under quarantine for 14 days from last exposure to the individual with confirmed COVID-19, either at home or at designated government quarantine facilities.
T63 3711-3888 Sentence denotes We monitored their health status daily; people who developed symptoms were conveyed in dedicated ambulances to hospital for isolation and testing as part of active case-finding.
T64 3889-4057 Sentence denotes We video-called individuals who were quarantined at home three times a day to verify their location; quarantine violators were tagged with a continuous tracking device.
T65 4058-4226 Sentence denotes We placed other contacts (depending on risk stratification) on phone surveillance or advised them to self-monitor and visit a primary-care clinic if they became unwell.
T66 4228-4247 Sentence denotes Clinical management
T67 4248-4344 Sentence denotes We isolated people with confirmed COVID-19 in individual negative-pressure rooms with anterooms.
T68 4345-4499 Sentence denotes We did blood investigations including a complete blood count, renal and liver function tests, and amounts of C-reactive protein and lactate dehydrogenase.
T69 4500-4621 Sentence denotes Treatment was mainly supportive; we started some patients on oral lopinavir (400 mg) with ritonavir (100 mg) twice daily.
T70 4622-4807 Sentence denotes We obtained clinical data for chronic medical illnesses, physical examinations, laboratory and radiological results, and clinical progression and outcome from inpatient medical records.
T71 4809-4846 Sentence denotes Analysis of disease transmission data
T72 4847-4992 Sentence denotes We reported the median (IQR) incubation period, defined as the duration between estimated dates of infection and reported symptom onset, using R.
T73 4993-5083 Sentence denotes We reported the serial interval range between transmission pairs in the household cluster.
T74 5084-5268 Sentence denotes We also calculated the probable number of transmissions arising from each confirmed case of COVID-19 by assuming that there was one unknown primary case for each of the three clusters.
T75 5270-5296 Sentence denotes Role of the funding source
T76 5297-5328 Sentence denotes This study received no funding.
T77 5329-5468 Sentence denotes The corresponding authors had full access to all data in the study and had final responsibility for the decision to submit for publication.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 442-451 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 1919-1928 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090