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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
106 8242-8294 Species denotes Middle East respiratory syndrome-related coronavirus Tax:1335626
147 9774-9779 Species denotes Human Tax:9606
4 17-22 Species denotes human Tax:9606
5 26-31 Species denotes human Tax:9606
6 54-76 Species denotes 2019 novel coronavirus Tax:2697049
7 78-87 Species denotes 2019-nCoV Tax:2697049
18 201-218 Species denotes novel coronavirus Tax:2697049
19 220-229 Species denotes 2019-nCoV Tax:2697049
20 338-347 Species denotes 2019-nCoV Tax:2697049
21 442-447 Species denotes human Tax:9606
22 451-456 Species denotes human Tax:9606
23 537-590 Species denotes severe acute respiratory syndrome-related coronavirus Tax:694009
24 592-600 Species denotes SARS-CoV Tax:694009
25 615-624 Species denotes influenza Tax:11308
26 247-266 Disease denotes respiratory disease MESH:D012140
27 278-287 Disease denotes pneumonia MESH:D011014
37 891-908 Species denotes novel coronavirus Tax:2697049
38 910-919 Species denotes 2019-nCoV Tax:2697049
39 1536-1541 Species denotes human Tax:9606
40 1545-1550 Species denotes human Tax:9606
41 1567-1576 Species denotes 2019-nCoV Tax:2697049
42 1872-1881 Species denotes 2019-nCoV Tax:2697049
43 1947-1956 Species denotes 2019-nCoV Tax:2697049
44 751-760 Disease denotes pneumonia MESH:D011014
45 1028-1036 Disease denotes zoonotic MESH:D015047
49 2161-2170 Species denotes 2019-nCoV Tax:2697049
50 2446-2451 Species denotes human Tax:9606
51 2455-2460 Species denotes human Tax:9606
53 4704-4712 Disease denotes zoonotic MESH:D015047
55 4324-4346 Species denotes 2019 novel coronavirus Tax:2697049
61 5905-5908 Gene denotes ABC
62 4915-4920 Species denotes human Tax:9606
63 5403-5412 Species denotes 2019-nCoV Tax:2697049
64 4896-4904 Disease denotes zoonotic MESH:D015047
65 5735-5743 Disease denotes infected MESH:D007239
71 6405-6410 Species denotes human Tax:9606
72 6414-6419 Species denotes human Tax:9606
73 6436-6445 Species denotes 2019-nCoV Tax:2697049
74 6360-6368 Disease denotes infected MESH:D007239
75 6934-6942 Disease denotes zoonotic MESH:D015047
77 7037-7059 Species denotes 2019 novel coronavirus Tax:2697049
80 7142-7147 Species denotes human Tax:9606
81 7151-7156 Species denotes human Tax:9606
83 7440-7462 Species denotes 2019 novel coronavirus Tax:2697049
101 7853-7866 Species denotes coronaviruses Tax:11118
102 7975-7984 Species denotes 2019-nCoV Tax:2697049
103 8165-8170 Species denotes human Tax:9606
104 8174-8179 Species denotes human Tax:9606
105 8196-8204 Species denotes SARS-CoV Tax:694009
107 8296-8304 Species denotes MERS-CoV Tax:1335626
108 8325-8333 Species denotes MERS-CoV Tax:1335626
109 8428-8433 Species denotes human Tax:9606
110 8534-8542 Species denotes MERS-CoV Tax:1335626
111 8569-8574 Species denotes human Tax:9606
112 8578-8583 Species denotes human Tax:9606
113 8668-8676 Species denotes SARS-CoV Tax:694009
114 8725-8730 Species denotes human Tax:9606
115 8734-8739 Species denotes human Tax:9606
116 8968-8977 Species denotes 2019-nCoV Tax:2697049
117 8992-9001 Species denotes 2019-nCoV Tax:2697049
119 9142-9164 Species denotes 2019 novel coronavirus Tax:2697049
122 9207-9259 Species denotes Middle East respiratory syndrome-related coronavirus Tax:1335626
123 9267-9320 Species denotes severe acute respiratory syndrome-related coronavirus Tax:694009
128 9549-9554 Species denotes human Tax:9606
129 9558-9563 Species denotes human Tax:9606
130 9580-9588 Species denotes SARS-CoV Tax:694009
131 9635-9644 Species denotes influenza Tax:11308
146 9673-9682 Species denotes 2019-nCoV Tax:2697049
148 9783-9788 Species denotes human Tax:9606
149 9805-9822 Species denotes influenza viruses Tax:11308
150 10009-10014 Species denotes human Tax:9606
151 10194-10207 Species denotes coronaviruses Tax:11118
152 10220-10237 Species denotes influenza viruses Tax:11308
153 10276-10285 Species denotes 2019-nCoV Tax:2697049
154 10522-10531 Species denotes 2019-nCoV Tax:2697049
155 10570-10579 Species denotes 2019-nCoV Tax:2697049
156 10587-10592 Species denotes human Tax:9606
157 9731-9740 Species denotes influenza Tax:11308
158 9988-9997 Species denotes influenza Tax:11308
159 10078-10087 Species denotes influenza Tax:11308
161 11540-11548 Disease denotes infected MESH:D007239
169 12276-12285 Species denotes 2019-nCoV Tax:2697049
170 12451-12456 Species denotes human Tax:9606
171 12636-12641 Species denotes human Tax:9606
172 12645-12650 Species denotes human Tax:9606
173 12671-12680 Species denotes 2019-nCoV Tax:2697049
174 12841-12854 Species denotes coronaviruses Tax:11118
175 12377-12385 Disease denotes zoonotic MESH:D015047
184 13304-13309 Species denotes human Tax:9606
185 13313-13318 Species denotes human Tax:9606
186 13335-13344 Species denotes 2019-nCoV Tax:2697049
187 13363-13371 Species denotes SARS-CoV Tax:694009
188 13486-13495 Species denotes 2019-nCoV Tax:2697049
189 13746-13754 Species denotes SARS-CoV Tax:694009
190 14213-14222 Species denotes 2019-nCoV Tax:2697049
191 13795-13804 Disease denotes infection MESH:D007239
194 14444-14447 Gene denotes CLA Gene:6404
195 14381-14384 Gene denotes CLA Gene:6404

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 5413-5420 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 4563-4568 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T2 6913-6918 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 247-266 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T2 278-287 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T3 537-570 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 592-600 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 615-624 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T6 751-760 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T7 2278-2288 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T8 8196-8204 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 8668-8676 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 9261-9265 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T11 9267-9300 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T12 9580-9588 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 9635-9644 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T14 9731-9740 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T15 9805-9814 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T16 9988-9997 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T17 10078-10087 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 10220-10229 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 13363-13371 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 13746-13754 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 13795-13804 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 17-22 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T2 26-31 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 157-160 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 179-180 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 199-200 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 442-447 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T7 451-456 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T8 637-638 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 701-713 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T10 738-739 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 822-823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 889-890 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1007-1008 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1060-1061 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1093-1100 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T16 1128-1131 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T17 1359-1362 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 1536-1541 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T19 1545-1550 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T20 1753-1754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2303-2304 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2446-2451 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T23 2455-2460 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T24 2766-2767 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 2813-2814 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 2865-2866 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 2963-2964 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2994-2995 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3044-3045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3131-3132 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 3242-3245 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T32 3333-3334 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 3460-3461 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3654-3655 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 3844-3845 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 3872-3873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 3926-3927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 4063-4064 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 4488-4490 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T40 4673-4678 http://purl.obolibrary.org/obo/CLO_0001404 denotes 50 6
T41 4780-4781 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 4905-4911 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T43 4915-4920 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T44 5169-5170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 5308-5311 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T46 5308-5311 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T47 5333-5335 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T48 5400-5402 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T49 5488-5490 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T50 5549-5550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 5717-5718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 5797-5799 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T53 5850-5851 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 6027-6036 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T55 6194-6196 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T56 6378-6380 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T57 6405-6410 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T58 6414-6419 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T59 6611-6612 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 6874-6876 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T61 7082-7084 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T62 7142-7147 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T63 7151-7156 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T64 7221-7222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 7277-7278 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 7365-7366 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 7690-7691 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 7740-7742 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T69 7814-7821 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T70 8147-8155 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T71 8165-8170 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T72 8174-8179 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T73 8418-8424 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T74 8428-8433 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T75 8569-8574 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T76 8578-8583 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T77 8604-8605 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 8725-8730 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T79 8734-8739 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T80 9015-9016 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 9088-9089 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 9185-9187 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T83 9487-9488 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 9549-9554 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T85 9558-9563 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T86 9774-9779 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T87 9783-9788 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T88 9815-9822 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T89 9875-9876 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 9905-9906 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 10009-10014 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T92 10230-10237 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T93 10587-10592 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T94 10668-10673 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T95 11173-11178 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T96 11327-11329 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T97 11967-11969 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T98 12040-12043 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T99 12111-12112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 12441-12447 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T101 12451-12456 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T102 12582-12583 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 12636-12641 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T104 12645-12650 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T105 12696-12701 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T106 13021-13022 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 13133-13134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 13304-13309 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T109 13313-13318 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T110 13755-13758 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 3006-3015 Chemical denotes explosive http://purl.obolibrary.org/obo/CHEBI_63490
T2 3821-3826 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T3 4736-4739 Chemical denotes Dec http://purl.obolibrary.org/obo/CHEBI_23574|http://purl.obolibrary.org/obo/CHEBI_23580
T5 5905-5908 Chemical denotes ABC http://purl.obolibrary.org/obo/CHEBI_421707
T6 13588-13597 Chemical denotes explosive http://purl.obolibrary.org/obo/CHEBI_63490
T7 14381-14384 Chemical denotes CLA http://purl.obolibrary.org/obo/CHEBI_3732|http://purl.obolibrary.org/obo/CHEBI_61159
T9 14444-14447 Chemical denotes CLA http://purl.obolibrary.org/obo/CHEBI_3732|http://purl.obolibrary.org/obo/CHEBI_61159

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 312-324 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T2 2191-2203 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T3 3142-3148 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T4 4458-4470 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T5 7108-7120 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-119 Sentence denotes Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020
T2 121-129 Sentence denotes Abstract
T3 130-288 Sentence denotes Since December 2019, China has been experiencing a large outbreak of a novel coronavirus (2019-nCoV) which can cause respiratory disease and severe pneumonia.
T4 289-392 Sentence denotes We estimated the basic reproduction number R0 of 2019-nCoV to be around 2.2 (90% high density interval:
T5 393-470 Sentence denotes 1.4–3.8), indicating the potential for sustained human-to-human transmission.
T6 471-661 Sentence denotes Transmission characteristics appear to be of similar magnitude to severe acute respiratory syndrome-related coronavirus (SARS-CoV) and pandemic influenza, indicating a risk of global spread.
T7 663-816 Sentence denotes On 31 December 2019, the World Health Organization (WHO) was alerted about a cluster of pneumonia of unknown aetiology in the city of Wuhan, China [1,2].
T8 817-964 Sentence denotes Only a few days later, Chinese authorities identified and characterised a novel coronavirus (2019-nCoV) as the causative agent of the outbreak [3].
T9 965-1248 Sentence denotes The outbreak appears to have started from a single or multiple zoonotic transmission events at a wet market in Wuhan where game animals and meat were sold [4] and has resulted in 5,997 confirmed cases in China and 68 confirmed cases in several other countries by 29 January 2020 [5].
T10 1249-1400 Sentence denotes Based on the number of exported cases identified in other countries, the actual size of the epidemic in Wuhan has been estimated to be much larger [6].
T11 1401-1577 Sentence denotes At this early stage of the outbreak, it is important to gain understanding of the transmission pattern and the potential for sustained human-to-human transmission of 2019-nCoV.
T12 1578-1882 Sentence denotes Information on the transmission characteristics will help coordinate current screening and containment strategies, support decision making on whether the outbreak constitutes a public health emergency of international concern (PHEIC), and is key for anticipating the risk of pandemic spread of 2019-nCoV.
T13 1883-2087 Sentence denotes In order to better understand the early transmission pattern of 2019-nCoV, we performed stochastic simulations of early outbreak trajectories that are consistent with the epidemiological findings to date.
T14 2089-2108 Sentence denotes Epidemic parameters
T15 2109-2171 Sentence denotes Two key properties will determine further spread of 2019-nCoV.
T16 2172-2390 Sentence denotes Firstly, the basic reproduction number R0 describes the average number of secondary cases generated by an infectious index case in a fully susceptible population, as was the case during the early phase of the outbreak.
T17 2391-2520 Sentence denotes If R0 is above the critical threshold of 1, continuous human-to-human transmission with sustained transmission chains will occur.
T18 2521-2705 Sentence denotes Secondly, the individual variation in the number of secondary cases provides further information about the expected outbreak dynamics and the potential for superspreading events [7-9].
T19 2706-2927 Sentence denotes If the dispersion of the number of secondary cases is high, a small number of cases may be responsible for a disproportionate number of secondary cases, while a large number of cases will not transmit the pathogen at all.
T20 2928-3089 Sentence denotes While superspreading always remain a rare event, it can result in a large and explosive transmission event and have a lot of impact on the course of an epidemic.
T21 3090-3236 Sentence denotes Conversely, low dispersion would lead to a steadier growth of the epidemic, with more homogeneity in the number of secondary cases per index case.
T22 3237-3289 Sentence denotes This has important implications for control efforts.
T23 3291-3329 Sentence denotes Simulating early outbreak trajectories
T24 3330-3394 Sentence denotes In a first step, we initialised simulations with one index case.
T25 3395-3539 Sentence denotes For each primary case, we generated secondary cases according to a negative-binomial offspring distribution with mean R0 and dispersion k [7,8].
T26 3540-3771 Sentence denotes The dispersion parameter k quantifies the variability in the number of secondary cases, and can be interpreted as a measure of the impact of superspreading events (the lower the value of k, the higher the impact of superspreading).
T27 3772-3913 Sentence denotes The generation time interval D was assumed to be gamma-distributed with a shape parameter of 2, and a mean that varied between 7 and 14 days.
T28 3914-4042 Sentence denotes We explored a wide range of parameter combinations (Table) and ran 1,000 stochastic simulations for each individual combination.
T29 4043-4246 Sentence denotes This corresponds to a total of 3.52 million one-index-case simulations that were run on UBELIX (http://www.id.unibe.ch/hpc), the high performance computing cluster at the University of Bern, Switzerland.
T30 4247-4373 Sentence denotes Table Parameter ranges for stochastic simulations of outbreak trajectories, 2019 novel coronavirus outbreak, China, 2019–2020
T31 4374-4447 Sentence denotes Parameter Description Range Number of values explored within the range
T32 4448-4504 Sentence denotes R0 Basic reproduction number 0.8–5.0 22 (equidistant)
T33 4505-4569 Sentence denotes k Dispersion parameter 0.0110 20 (equidistant on log10 scale)
T34 4570-4636 Sentence denotes D Generation time interval (days) 9–11,13,16–19 8 (equidistant)
T35 4637-4692 Sentence denotes n Initial number of index cases 1–50 6 (equidistant)
T36 4693-4962 Sentence denotes T Date of zoonotic transmission 20 Nov–4 Dec 2019 Randomised for each index case In a second step, we accounted for the uncertainty regarding the number of index cases n and the date T of the initial zoonotic animal-to-human transmissions at the wet market in Wuhan.
T37 4963-5095 Sentence denotes An epidemic with several index cases can be considered as the aggregation of several independent epidemics with one index case each.
T38 5096-5249 Sentence denotes We sampled (with replacement) n of the one-index-case epidemics, sampled a date of onset for each index case and aggregated the epidemic curves together.
T39 5250-5426 Sentence denotes The sampling of the date of onset was done uniformly from a 2-week interval around 27 November 2019, in coherence with early phylogenetic analyses of 11 2019-nCoV genomes [10].
T40 5427-5639 Sentence denotes This step was repeated 100 times for each combination of R0 (22 points), k (20 points), D (8 points) and n (6 points) for a total of 2,112,000 full epidemics simulated that included the uncertainty on D, n and T.
T41 5640-5846 Sentence denotes Finally, we calculated the proportion of stochastic simulations that reached a total number of infected cases within the interval between 1,000 and 9,700 by 18 January 2020, as estimated by Imai et al. [6].
T42 5847-6102 Sentence denotes In a process related to approximate Bayesian computation (ABC), the parameter value combinations that led to simulations within that interval were treated as approximations to the posterior distributions of the parameters with uniform prior distributions.
T43 6103-6198 Sentence denotes Model simulations and analyses were performed in the R software for statistical computing [11].
T44 6199-6257 Sentence denotes Code files are available on https://github.com/jriou/wcov.
T45 6259-6317 Sentence denotes Transmission characteristics of the 2019 novel coronavirus
T46 6318-6537 Sentence denotes In order to reach between 1,000 and 9,700 infected cases by 18 January 2020, the early human-to-human transmission of 2019-nCoV was characterised by values of R0 around 2.2 (median value, with 90% high density interval:
T47 6538-6558 Sentence denotes 1.4–3.8) (Figure 1).
T48 6559-6674 Sentence denotes The observed data at this point are compatible with a large range of values for the dispersion parameter k (median:
T49 6675-6707 Sentence denotes 0.54, 90% high density interval:
T50 6708-6720 Sentence denotes 0.014–6.95).
T51 6721-6796 Sentence denotes However, our simulations suggest that very low values of k are less likely.
T52 6797-6960 Sentence denotes These estimates incorporate the uncertainty about the total epidemic size on 18 January 2020 and about the date and scale of the initial zoonotic event (Figure 2).
T53 6961-7097 Sentence denotes Figure 1 Values of R0 and k most compatible with the estimated size of the 2019 novel coronavirus epidemic in China, on 18 January 2020
T54 7098-7170 Sentence denotes The basic reproduction number R0 quantifies human-to-human transmission.
T55 7171-7317 Sentence denotes The dispersion parameter k quantifies the risk of a superspreading event (lower values of k are linked to a higher probability of superspreading).
T56 7318-7388 Sentence denotes Note that the probability density of k implies a log10 transformation.
T57 7389-7489 Sentence denotes Figure 2 Illustration of the simulation strategy, 2019 novel coronavirus outbreak, China, 2019–2020
T58 7490-7581 Sentence denotes The lines represent the cumulative incidence of 480 simulations with R0 = 1.8 and k = 1.13.
T59 7582-7643 Sentence denotes The other parameters are left to vary according to the Table.
T60 7644-7765 Sentence denotes Among these simulated epidemics, 54.3% led to a cumulative incidence between 1,000 and 9,700 on 18 January 2020 (in red).
T61 7767-7821 Sentence denotes Comparison with past emergences of respiratory viruses
T62 7822-7985 Sentence denotes Comparison with other emerging coronaviruses in the past allows to put into perspective the available information regarding the transmission patterns of 2019-nCoV.
T63 7986-8081 Sentence denotes Figure 3 shows the combinations of R0 and k that are most likely at this stage of the epidemic.
T64 8082-8310 Sentence denotes Our estimates of R0 and k are more similar to previous estimates focusing on early human-to-human transmission of SARS-CoV in Beijing and Singapore [7] than of Middle East respiratory syndrome-related coronavirus (MERS-CoV) [9].
T65 8311-8533 Sentence denotes The spread of MERS-CoV was characterised by small clusters of transmission following repeated instances of animal-to-human transmission events, mainly driven by the occurrence of superspreading events in hospital settings.
T66 8534-8627 Sentence denotes MERS-CoV could however not sustain human-to-human transmission beyond a few generations [12].
T67 8628-8792 Sentence denotes Conversely, the international spread of SARS-CoV lasted for 9 months and was driven by sustained human-to-human transmission, with occasional superspreading events.
T68 8793-8923 Sentence denotes It led to more than 8,000 cases around the world and required extensive efforts by public health authorities to be contained [13].
T69 8924-9030 Sentence denotes Our assessment of the early transmission of 2019-nCoV suggests that 2019-nCoV might follow a similar path.
T70 9031-9200 Sentence denotes Figure 3 Proportion of simulated epidemics that lead to a cumulative incidence between 1,000 and 9,700 of the 2019 novel coronavirus outbreak, China, on 18 January 2020
T71 9201-9206 Sentence denotes MERS:
T72 9207-9321 Sentence denotes Middle East respiratory syndrome-related coronavirus; SARS: severe acute respiratory syndrome-related coronavirus.
T73 9322-9483 Sentence denotes This can be interpreted as the combinations of R0 and k values most compatible with the estimation of epidemic size before quarantine measures were put in place.
T74 9484-9654 Sentence denotes As a comparison, we show the estimates of R0 and k for the early human-to-human transmission of SARS-CoV in Singapore and Beijing and of 1918 pandemic influenza [7,9,14].
T75 9655-9773 Sentence denotes Our estimates for 2019-nCoV are also compatible with those of 1918 pandemic influenza, for which k was estimated [14].
T76 9774-9955 Sentence denotes Human-to-human transmission of influenza viruses is characterised by R0 values between 1.5 and 2 and a larger value of k, implying a more steady transmission without superspreading.
T77 9956-10174 Sentence denotes The emergence of new strains of influenza, for which human populations carried little to no immunity contrary to seasonal influenza, led to pandemics with different severity such as the ones in1918, 1957 1968 and 2009.
T78 10175-10412 Sentence denotes It is notable that coronaviruses differ from influenza viruses in many aspects, and evidence for the 2019-nCoV with respect to case fatality rate, transmissibility from asymptomatic individuals and speed of transmission is still limited.
T79 10413-10674 Sentence denotes Without speculating about possible consequences, the values of R0 and k found here during the early stage of 2019-nCoV emergence and the lack of immunity to 2019-nCoV in the human population leave open the possibility for pandemic circulation of this new virus.
T80 10676-10701 Sentence denotes Strengths and limitations
T81 10702-10924 Sentence denotes The scarcity of available data, especially on case counts by date of disease onset as well as contact tracing, greatly limits the precision of our estimates and does not yet allow for reliable forecasts of epidemic spread.
T82 10925-11088 Sentence denotes Case counts provided by local authorities in the early stage of an emerging epidemic are notoriously unreliable as reporting rates are unstable and vary with time.
T83 11089-11237 Sentence denotes This is due to many factors such as the initial lack of proper diagnosis tools, the focus on the more severe cases or the overcrowding of hospitals.
T84 11238-11444 Sentence denotes We avoided this surveillance bias by relying on an indirect estimate of epidemic size on 18 January, based on cases identified in foreign countries before quarantine measures were implemented on 23 January.
T85 11445-11628 Sentence denotes This estimated range of epidemic size relies itself on several assumptions, including that all infected individuals who travelled from Wuhan to other countries have been detected [6].
T86 11629-11764 Sentence denotes This caveat may lead to an underestimation of transmissibility, especially considering the recent reports about asymptomatic cases [4].
T87 11765-11978 Sentence denotes Conversely, our results do not depend on any assumption about the existence of asymptomatic transmission, and only reflect the possible combinations of transmission events that lead to the situation on 18 January.
T88 11979-12068 Sentence denotes Our analysis, while limited because of the scarcity of data, has two important strengths.
T89 12069-12515 Sentence denotes Firstly, it is based on the simulation of a wide range of possibilities regarding epidemic parameters and allows for the full propagation on the final estimates of the many remaining uncertainties regarding 2019-nCoV and the situation in Wuhan: on the actual size of the epidemic, on the size of the initial zoonotic event at the wet market, on the date(s) of the initial animal-to-human transmission event(s) and on the generation time interval.
T90 12516-12681 Sentence denotes As it accounts for all these uncertainties, our analysis provides a summary of the current state of knowledge about the human-to-human transmissibility of 2019-nCoV.
T91 12682-12861 Sentence denotes Secondly, its focus on the possibility of superspreading events by using negative-binomial offspring distributions appears relevant in the context of emerging coronaviruses [7,8].
T92 12862-13061 Sentence denotes While our estimate of k remains imprecise, the simulations suggest that very low values of k < 0.1 are less likely than higher values < 0.1 that correspond to a more homogeneous transmission pattern.
T93 13062-13242 Sentence denotes However, values of k in the range of 0.1–0.2 are still compatible with a small risk of occurrence of large superspreading events, especially impactful in hospital settings [15,16].
T94 13244-13255 Sentence denotes Conclusions
T95 13256-13390 Sentence denotes Our analysis suggests that the early pattern of human-to-human transmission of 2019-nCoV is reminiscent of SARS-CoV emergence in 2002.
T96 13391-13496 Sentence denotes International collaboration and coordination will be crucial in order to contain the spread of 2019-nCoV.
T97 13497-13716 Sentence denotes At this stage, particular attention should be given to the prevention of possible rare but explosive superspreading events, while the establishment of sustained transmission chains from single cases cannot be ruled out.
T98 13717-13941 Sentence denotes The previous experience with SARS-CoV has shown that established practices of infection control, such as early detection and isolation, contact tracing and the use of personal protective equipment, can stop such an epidemic.
T99 13942-14223 Sentence denotes Given the existing uncertainty around the case fatality rate and transmission, our findings confirm the importance of screening, surveillance and control efforts, particularly at airports and other transportation hubs, in order to prevent further international spread of 2019-nCoV.
T100 14225-14241 Sentence denotes Acknowledgements
T101 14242-14311 Sentence denotes JR is funded by the Swiss National Science Foundation (grant 174281).
T102 14313-14334 Sentence denotes Conflict of interest:
T103 14335-14349 Sentence denotes None declared.
T104 14350-14510 Sentence denotes Authors’ contributions: JR and CLA designed the study, JR performed model simulations, JR and CLA analysed and interpreted the results and wrote the manuscript.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 278-287 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 751-760 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32019669-16292310-29338347 2700-2701 16292310 denotes 7
32019669-25932579-29338347 2700-2701 25932579 denotes 7
32019669-26132768-29338347 2700-2701 26132768 denotes 7
32019669-16292310-29338348 3534-3535 16292310 denotes 7
32019669-25932579-29338349 3536-3537 25932579 denotes 8
32019669-16292310-29338350 8231-8232 16292310 denotes 7
32019669-26132768-29338351 8307-8308 26132768 denotes 9
32019669-23831141-29338352 8623-8625 23831141 denotes 12
32019669-17568476-29338353 8919-8921 17568476 denotes 13
32019669-16292310-29338354 9646-9647 16292310 denotes 7
32019669-26132768-29338355 9648-9649 26132768 denotes 9
32019669-21749971-29338356 9650-9652 21749971 denotes 14
32019669-21749971-29338357 9769-9771 21749971 denotes 14
32019669-31986261-29338358 11761-11762 31986261 denotes 4
32019669-16292310-29338359 12856-12857 16292310 denotes 7
32019669-25932579-29338360 12858-12859 25932579 denotes 8
32019669-26539018-29338361 13235-13237 26539018 denotes 15
32019669-23782161-29338362 13238-13240 23782161 denotes 16

MyTest

Id Subject Object Predicate Lexical cue
32019669-16292310-29338347 2700-2701 16292310 denotes 7
32019669-25932579-29338347 2700-2701 25932579 denotes 7
32019669-26132768-29338347 2700-2701 26132768 denotes 7
32019669-16292310-29338348 3534-3535 16292310 denotes 7
32019669-25932579-29338349 3536-3537 25932579 denotes 8
32019669-16292310-29338350 8231-8232 16292310 denotes 7
32019669-26132768-29338351 8307-8308 26132768 denotes 9
32019669-23831141-29338352 8623-8625 23831141 denotes 12
32019669-17568476-29338353 8919-8921 17568476 denotes 13
32019669-16292310-29338354 9646-9647 16292310 denotes 7
32019669-26132768-29338355 9648-9649 26132768 denotes 9
32019669-21749971-29338356 9650-9652 21749971 denotes 14
32019669-21749971-29338357 9769-9771 21749971 denotes 14
32019669-31986261-29338358 11761-11762 31986261 denotes 4
32019669-16292310-29338359 12856-12857 16292310 denotes 7
32019669-25932579-29338360 12858-12859 25932579 denotes 8
32019669-26539018-29338361 13235-13237 26539018 denotes 15
32019669-23782161-29338362 13238-13240 23782161 denotes 16