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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 45-64 Disease denotes coronavirus disease MESH:D018352
3 66-74 Disease denotes COVID-19 MESH:C000657245
5 166-174 Disease denotes COVID-19 MESH:C000657245
11 1042-1048 Species denotes people Tax:9606
12 658-677 Disease denotes coronavirus disease MESH:D018352
13 679-687 Disease denotes COVID-19 MESH:C000657245
14 1285-1293 Disease denotes COVID-19 MESH:C000657245
15 1302-1308 Disease denotes deaths MESH:D003643
26 2759-2766 Species denotes persons Tax:9606
27 2786-2793 Species denotes persons Tax:9606
28 2824-2831 Species denotes persons Tax:9606
29 2956-2963 Species denotes persons Tax:9606
30 3119-3126 Species denotes Persons Tax:9606
31 2255-2263 Disease denotes COVID-19 MESH:C000657245
32 2488-2497 Disease denotes infection MESH:D007239
33 2947-2955 Disease denotes infected MESH:D007239
34 3015-3025 Disease denotes infections MESH:D007239
35 3145-3155 Disease denotes infections MESH:D007239
41 3528-3535 Species denotes persons Tax:9606
43 3340-3348 Disease denotes COVID-19 MESH:C000657245
45 3693-3712 Disease denotes coronavirus disease MESH:D018352
47 3845-3846 Gene denotes τ Gene:4137
50 4091-4092 Gene denotes 𝜏 Gene:4137
51 4288-4292 Gene denotes ship Gene:3635
55 5497-5504 Species denotes persons Tax:9606
56 5546-5553 Species denotes persons Tax:9606
57 5593-5600 Species denotes persons Tax:9606
64 5861-5868 Species denotes persons Tax:9606
65 6158-6165 Species denotes persons Tax:9606
66 6195-6202 Species denotes persons Tax:9606
67 6311-6318 Species denotes persons Tax:9606
68 6075-6095 Disease denotes secondary infections MESH:D060085
69 6302-6310 Disease denotes infected MESH:D007239
72 6676-6683 Species denotes persons Tax:9606
73 6597-6605 Disease denotes COVID-19 MESH:C000657245
75 6825-6844 Disease denotes coronavirus disease MESH:D018352
81 8091-8098 Species denotes persons Tax:9606
82 7725-7735 Disease denotes infections MESH:D007239
83 8260-8270 Disease denotes infections MESH:D007239
84 8363-8373 Disease denotes infections MESH:D007239
85 8576-8596 Disease denotes secondary infections MESH:D060085
90 8917-8923 Species denotes people Tax:9606
91 8978-8985 Species denotes persons Tax:9606
92 8738-8746 Disease denotes infected MESH:D007239
93 9080-9090 Disease denotes infections MESH:D007239
95 9467-9477 Disease denotes infections MESH:D007239
97 10178-10186 Disease denotes COVID-19 MESH:C000657245
99 10306-10325 Disease denotes coronavirus disease MESH:D018352
105 12388-12395 Species denotes persons Tax:9606
106 12534-12541 Species denotes persons Tax:9606
107 11737-11745 Disease denotes COVID-19 MESH:C000657245
108 12403-12423 Disease denotes secondary infections MESH:D060085
109 12525-12533 Disease denotes infected MESH:D007239
119 12809-12814 Species denotes human Tax:9606
120 12818-12823 Species denotes human Tax:9606
121 14556-14562 Species denotes people Tax:9606
122 14985-14992 Species denotes persons Tax:9606
123 16299-16306 Species denotes persons Tax:9606
124 13672-13682 Disease denotes infections MESH:D007239
125 15403-15411 Disease denotes COVID-19 MESH:C000657245
126 15856-15864 Disease denotes COVID-19 MESH:C000657245
127 16290-16298 Disease denotes infected MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 10742-10746 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T2 14085-14089 Body_part denotes face http://purl.org/sig/ont/fma/fma24728

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 10848-10853 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T2 14085-14089 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p104057s49 13939-13946 NegReg denotes reduced

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 66-74 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 166-174 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 679-687 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 1285-1293 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 2119-2129 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T6 2255-2263 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 2311-2321 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T8 2488-2497 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T9 2515-2529 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T10 2915-2929 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T11 3015-3025 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T12 3145-3155 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T13 3340-3348 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 3459-3469 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T15 3494-3504 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T16 3683-3691 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 3901-3911 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T18 6085-6095 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T19 6147-6157 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T20 6184-6194 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T21 6577-6587 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T22 6597-6605 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 6815-6823 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 7148-7158 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T25 7725-7735 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T26 8260-8270 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T27 8363-8373 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T28 8586-8596 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T29 9080-9090 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T30 9467-9477 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T31 10178-10186 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 10296-10304 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 11737-11745 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T34 12413-12426 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T35 13672-13682 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T36 15403-15411 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 15856-15864 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 296-297 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 402-403 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 466-467 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 821-822 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 850-852 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T6 882-883 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1448-1451 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T8 1547-1548 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1571-1572 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2036-2037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2097-2098 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2184-2185 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2203-2206 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3-5
T14 2348-2349 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2584-2586 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T16 2691-2692 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2770-2771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 2887-2888 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 3829-3830 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 3874-3879 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T21 3922-3923 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 4115-4116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 4147-4148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 4518-4519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 4673-4674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 4951-4952 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 5040-5050 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T28 5211-5221 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T29 5253-5254 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 5260-5261 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T31 5327-5337 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T32 5359-5360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 5409-5415 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T34 5687-5688 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 5845-5846 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 6272-6273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 6374-6377 http://purl.obolibrary.org/obo/CLO_0002755 denotes D–F
T38 6489-6490 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T39 6540-6541 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T40 6620-6621 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 6642-6643 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 6654-6655 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 6846-6847 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 6873-6874 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 7062-7063 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T46 7124-7125 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T47 7179-7180 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 7292-7295 http://purl.obolibrary.org/obo/CLO_0002755 denotes D–F
T49 7639-7647 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremes
T50 7653-7654 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 7778-7779 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 7986-7998 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organisation
T53 8235-8239 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T54 8247-8249 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T55 8470-8471 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 8521-8522 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 8753-8756 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T58 8757-8758 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 8807-8808 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 8886-8887 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 9162-9171 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T62 9248-9249 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 9486-9488 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T64 9495-9496 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 9567-9568 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 9680-9681 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 9883-9884 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 10137-10138 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 10176-10177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 10199-10200 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 10343-10344 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T72 10381-10382 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T73 10504-10505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 10581-10582 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 10633-10634 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 10983-10984 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T77 11094-11095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 11114-11115 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 11309-11310 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 11372-11382 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T81 11707-11708 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 12108-12118 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T83 12268-12269 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 12366-12367 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 12427-12428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 12508-12512 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T87 12759-12760 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 12809-12814 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T89 12818-12823 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T90 12931-12932 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 13018-13019 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 13274-13275 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T93 13421-13424 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T94 13559-13560 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 13585-13586 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 13702-13703 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T97 14051-14052 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 14085-14089 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T99 14243-14244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 14273-14283 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T101 14365-14366 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 14429-14430 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 14673-14674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 15585-15591 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T105 15617-15624 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T106 15663-15670 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digital
T107 15744-15746 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T108 15815-15816 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 15890-15897 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 8012-8014 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T2 10713-10718 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T3 11458-11463 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T4 16390-16392 Chemical denotes HS http://purl.obolibrary.org/obo/CHEBI_74056
T5 16471-16473 Chemical denotes HS http://purl.obolibrary.org/obo/CHEBI_74056
T6 16520-16522 Chemical denotes SO http://purl.obolibrary.org/obo/CHEBI_45822
T7 16549-16551 Chemical denotes HS http://purl.obolibrary.org/obo/CHEBI_74056

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 13049-13058 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour

2_test

Id Subject Object Predicate Lexical cue
32265005-32199470-29326713 814-815 32199470 denotes 1
32265005-24060621-29326714 2203-2204 24060621 denotes 3
32265005-32074444-29326715 2330-2331 32074444 denotes 6
32265005-31995857-29326716 2332-2333 31995857 denotes 7
32265005-32183930-29326717 3113-3114 32183930 denotes 8
32265005-32179137-29326718 3115-3116 32179137 denotes 9
32265005-23665296-29326719 4176-4178 23665296 denotes 10
32265005-23665296-29326720 4311-4313 23665296 denotes 10
32265005-32109273-29326721 4314-4316 32109273 denotes 11
32265005-32227186-29326722 11781-11783 32227186 denotes 13
32265005-32181488-29326723 12889-12891 32181488 denotes 16
32265005-32164834-29326724 13382-13384 32164834 denotes 17
32265005-32181488-29326725 15383-15385 32181488 denotes 16
32265005-32149043-29326726 15744-15746 32149043 denotes 18
32265005-32125371-29326727 15780-15782 32125371 denotes 19
32265005-32167146-29326728 15796-15798 32167146 denotes 20

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-99 Sentence denotes Only strict quarantine measures can curb the coronavirus disease (COVID-19) outbreak in Italy, 2020
T2 101-109 Sentence denotes Abstract
T3 110-184 Sentence denotes Several Italian towns are under lockdown to contain the COVID-19 outbreak.
T4 185-315 Sentence denotes The level of transmission reduction required for physical distancing interventions to mitigate the epidemic is a crucial question.
T5 316-485 Sentence denotes We show that very high adherence to community quarantine (total stay-home policy) and a small household size is necessary for curbing the outbreak in a locked-down town.
T6 486-588 Sentence denotes The larger the household size and amount of time in the public, the longer the lockdown period needed.
T7 590-608 Sentence denotes European epicentre
T8 609-817 Sentence denotes In February 2020, Italy became the epicentre for coronavirus disease (COVID-19) in Europe, with many exportations to other countries, and widespread community transmission, particularly in Northern Italy [1].
T9 818-1020 Sentence denotes As a public health response, on 22 February 2020, Italy imposed a lockdown with shutdown of businesses, schools and public places plus physical distancing in ‘hotspot’ regions close to Milan and Venice.
T10 1021-1150 Sentence denotes Approximately 50,000 people could not enter or leave several towns in Veneto and Lombardy for 14 days without special permission.
T11 1151-1228 Sentence denotes The population sizes in these towns range from 927 to 15,293 individuals [2].
T12 1229-1439 Sentence denotes As at 9 March 2020, 7,375 laboratory-confirmed cases of COVID-19 and 366 deaths had been observed in Italy, so on that date, the community quarantine was extended to include all of Northern Italy until 3 April.
T13 1440-1614 Sentence denotes Here we aim to investigate the extent of physical distancing needed to effectively control the outbreak in a lockdown situation in a small size town setting typical of Italy.
T14 1615-1834 Sentence denotes We specifically estimate the disease burden and the time required until the quarantine can be lifted, by taking into account the time spent by individuals in the public (i.e. outside of the home) and the household size.
T15 1836-1873 Sentence denotes Stochastic individual based processes
T16 1874-2223 Sentence denotes To account for the importance of stochasticity in individual-based processes within smaller cities and within households, we modelled the outbreak progression as a continuous-time Markov process, specifically by developing a susceptible-exposed-infectious-recovered (SEIR) epidemiological model in the form of a Master equation [3-5] (Supplement 1).
T17 2224-2335 Sentence denotes The model was parameterised to COVID-19 based on published data on incubation time and infectious period [6,7].
T18 2336-2726 Sentence denotes We modelled a scenario where 0.1% of the population in the quarantined town would be in the latent period (i.e. the period of time between the point of infection and the onset of infectiousness) at the time of implementing the quarantine policy on 22 February, and that all symptomatic cases would have been moved out the locked-down town (e.g. placed in a hospital for care and isolation).
T19 2727-2794 Sentence denotes This corresponds to five latent persons in a city of 5,000 persons.
T20 2795-2870 Sentence denotes Further, we assumed that all persons were isolated after 1 day of symptoms.
T21 2871-2939 Sentence denotes We also assumed a pre-symptomatic period of infectiousness of 1 day.
T22 2940-3118 Sentence denotes Of all infected persons, we modelled different proportions of asymptomatic infections (scenarios of 10%, 20% or 50%) based on our preliminary knowledge on such proportions [8,9].
T23 3119-3221 Sentence denotes Persons with asymptomatic infections would not be isolated and continue to contribute to transmission.
T24 3222-3261 Sentence denotes Parameters are summarised in the Table.
T25 3262-3383 Sentence denotes Table Most central parameters and corresponding values used for the model of COVID-19 outbreak progression in this study
T26 3384-3400 Sentence denotes Parameter Value
T27 3401-3429 Sentence denotes Incubation period in days 5
T28 3430-3458 Sentence denotes Latent period (𝐿) in days 4
T29 3459-3493 Sentence denotes Infectious period (1/𝛾) in days 2
T30 3494-3554 Sentence denotes Infectious period of asymptomatic persons (1/𝛾𝑎) in days 10
T31 3555-3599 Sentence denotes Proportion asymptomatic (𝑎) (0.1, 0.2, 0.5)
T32 3600-3640 Sentence denotes Within household contact-rate (𝑐) 2.1⁄𝜏
T33 3641-3682 Sentence denotes Public location contact-rate (𝑐̃) 0.27⁄𝜏
T34 3683-3713 Sentence denotes COVID-19: coronavirus disease.
T35 3714-3979 Sentence denotes The parameter γ denotes the daily rate of recovery from the disease, 𝛾𝑎 denotes the daily rate of removal to e.g., a hospital, and τ denotes the probability of virus transmission from an infectious person to a susceptible in the event of contact (See Supplement 1).
T36 3980-4371 Sentence denotes Importantly, the standard reproductive rate [5], equal to the product between contact rate and the probability 𝜏 of transmission given a contact event, was set within a household to β = cτ = 2.1 [10], and within public locations in the community to β~=c~τ=0.27; lower than in mainland China or on the cruise ship Diamond Princess [10,11], as population densities in European towns are lower.
T37 4372-4497 Sentence denotes The within-household contact-rate, 𝑐, was thus assumed to be eight times higher than the contact-rate 𝑐̃ at public locations.
T38 4498-4702 Sentence denotes We could then apply a quarantine adherence parameter 𝜑, to model dynamically the amount of time spent in households relative to that in public locations (see Supplement 1 for a more detailed description).
T39 4704-4724 Sentence denotes Quarantine scenarios
T40 4725-4888 Sentence denotes We modelled the effectiveness of quarantine based on the degree of adherence to quarantine, measured by the number of hours per person spent in the public per day.
T41 4889-5132 Sentence denotes Complete noncompliance to community quarantine corresponds to a reference quarantine level, where individuals perform their every-day out-of-household activities (i.e. working, shopping, socialising) as normal, for an average 10 hours per day.
T42 5133-5259 Sentence denotes Medium adherence to community quarantine restricts every-day out-of-household activities to 50% of normal, i.e. 5 hours a day.
T43 5260-5365 Sentence denotes A complete community quarantine corresponds to no out-of-household activities at all, i.e. 0 hours a day.
T44 5366-5643 Sentence denotes For any degree of quarantine adherence, we tested for four different average household sizes: (i) larger average households of six persons, (ii) medium average households of three persons, (iii) small average households of two persons, and lastly (iv) single-person households.
T45 5644-5946 Sentence denotes Given that Italy had initially implemented a 14-days lockdown with community quarantine in several towns in Northern Italy, we estimated the number of secondary cases, including asymptomatic cases, in a town of 5,000 persons by the end of this time period in relation to the above scenarios (Figure 1).
T46 5947-6238 Sentence denotes For any degree of quarantine adherence between 0 and 10 hours, Figure1A, Figure 1B and Figure 1C provide the expected number of secondary infections over 14 days of lockdown, and the number of latent infectious persons and the number of infectious persons respectively at Day 14 of lockdown.
T47 6239-6420 Sentence denotes These reported numbers relate to a population where 10% of all infected persons are asymptomatic, and would increase for 20% (Figure 1 D–F) or 50% (Figure 1 G–I) asymptomatic cases.
T48 6421-6814 Sentence denotes Figure 1 Estimation of the number of total secondary cases (panels A, D, G) during the 14-days period and the (panels B, E, H) latent and (panels C, F, I) infectious cases of COVID-19 at the end of a 14-days lockdown of a city with a population of 5,000 persons, depending on the degree of community quarantine adherencea, the size of quarantine units and the proportion of asymptomatic cases
T49 6815-6845 Sentence denotes COVID-19: coronavirus disease.
T50 6846-6966 Sentence denotes a Low adherence means that a large amount of time (up to 10 hours) is spent out of the household per day and per person.
T51 6967-7190 Sentence denotes Generally, higher adherence and smaller quarantine units help to minimise the number of (Panel A) secondary cases over the 14 days period, as well as (Panel B) latent and (Panel C) infectious cases at the end of a lockdown.
T52 7191-7233 Sentence denotes This was shown for 10% asymptomatic cases.
T53 7234-7360 Sentence denotes The same conclusion follows when also considering (Panels D–F) 20% asymptomatic cases and (Panels G–I) 50% asymptomatic cases.
T54 7361-7443 Sentence denotes The number of cases, however, increases with the proportion of asymptomatic cases.
T55 7444-7623 Sentence denotes Our model shows how the number of secondary cases within the town increases with the time spent in the public, and also with the average household size (i.e. the quarantine unit).
T56 7624-7760 Sentence denotes Looking at the extremes, for a six-person household and no community quarantine, we predicted 43 new infections over the 14 days period.
T57 7761-7924 Sentence denotes In contrast, for a single-person household and complete community quarantine (no time outside of homes), no secondary cases were predicted over the 14 days period.
T58 7925-8053 Sentence denotes The average household size in Italy is 2.58 according to the Organisation for Economic Co-operation and Development (OECD) [12].
T59 8054-8291 Sentence denotes For an average household size of two persons with complete, near-complete, medium and no community quarantine (i.e. 0, 1, 5, and 10 hours respectively in the community), we predict 3, 4, 7 and 11 secondary infections during the lockdown.
T60 8292-8402 Sentence denotes With an average three-person household size, 7, 8, 12 and 20 secondary infections are predicted, respectively.
T61 8403-8515 Sentence denotes The average Italian household size 2.58 is thus in-between that of a two-person and three-person household size.
T62 8516-8663 Sentence denotes With a six-person average household size, 16, 19, 29 and 43 secondary infections would be predicted to occur over the 14-days period, respectively.
T63 8664-8882 Sentence denotes In addition, our model indicates that the number of secondary, latent and infected cases has a linear relationship with the population size of a lockdown region, provided same population densities apply between cities.
T64 8883-9129 Sentence denotes In a locked-down area with 50,000 people, we would expect for an average household size of two persons with complete, near-complete, medium and no community quarantine 30, 40, 70 and 110 secondary infections over the 14-days period, respectively.
T65 9131-9157 Sentence denotes Duration of the quarantine
T66 9158-9270 Sentence denotes The objective of the lockdown with community quarantine is to contain the outbreak within a manageable duration.
T67 9271-9440 Sentence denotes Figure 2 shows the results on lockdown durations required for average household sizes of 1, 2, 3 and 6, and for various degrees of strictness of quarantine restrictions.
T68 9441-9652 Sentence denotes Assuming 10% asymptomatic infections (Figure 2a), for a three-person average household-size situation, around 30 days will be a sufficient length under conditions of near-complete community quarantine adherence.
T69 9653-9721 Sentence denotes With only medium adherence a duration of 54 days would be necessary.
T70 9722-9835 Sentence denotes Less strict quarantine will result in much longer lockdown periods, which then become unfeasible for any society.
T71 9836-9935 Sentence denotes These results are only marginally different to a situation with 50% asymptomatic cases (Figure 2b).
T72 9936-10087 Sentence denotes In addition, the definition to declare an outbreak over requires waiting two times the maximum incubation period after the last case, e.g. 2 × 14 days.
T73 10088-10295 Sentence denotes Figure 2 Estimation of the required duration of a lockdown with quarantine, to contain a COVID-19 outbreak in a city of 5,000 inhabitants, depending on the quarantine adherence strictness and household size
T74 10296-10326 Sentence denotes COVID-19: coronavirus disease.
T75 10327-10558 Sentence denotes Assuming (panel A) 10% asymptomatic cases, and (panel B) 50% asymptomatic cases respectively, the quarantine duration required to successfully curb the outbreak is presented as a function of time spent out of the household (hours).
T76 10559-10681 Sentence denotes This is based on that a period of at least 14 days since the last case is a sufficient criterium to suppress the outbreak.
T77 10682-10735 Sentence denotes Four different quarantine unit group-sizes are shown.
T78 10736-10825 Sentence denotes The y-axis was limited to 90 days to show the span within the most relevant time-horizon.
T79 10826-10930 Sentence denotes At this relevant time scale, there are only marginal differences between 10% and 50% asymptomatic cases.
T80 10932-10942 Sentence denotes Discussion
T81 10943-10982 Sentence denotes These findings have major implications.
T82 10983-11110 Sentence denotes A lockdown is designed to reduce spread beyond the lockdown area, and to also prevent further importation into a lockdown area.
T83 11111-11182 Sentence denotes In a lockdown area, all measures need to be taken to curb transmission.
T84 11183-11400 Sentence denotes We showed that transmission will continue to occur unless the most stringent community quarantine measures are being taken in a lockdown setting, which means near-complete reduction of all activities in the community.
T85 11401-11513 Sentence denotes We also find that smaller household sizes, or quarantine group sizes, are associated with fewer secondary cases.
T86 11514-11736 Sentence denotes Our model results apply to any small-city population size, and can be generalised to larger towns and cities given the linear relationship between population size and secondary cases, assuming a similar population density.
T87 11737-11785 Sentence denotes COVID-19 is driven by population densities [13].
T88 11786-11936 Sentence denotes For settings with higher population densities, which facilitate more intermixing within the population, higher number of secondary cases are expected.
T89 11937-12056 Sentence denotes The population density in urban Italy is 205.45/km2 [14] compared to Hubei Province, China, where it is 2,804/km2 [15].
T90 12057-12178 Sentence denotes We note that with near 100% restriction of outdoor activities, all transmission will continue to occur within households.
T91 12179-12450 Sentence denotes In the event of an average household size of three individuals, this would mean that, as a result of within-household transmission, seven secondary cases would be expected (Figure 1a) in a population of 5,000 persons, or 70 secondary infections in a population of 50,000.
T92 12451-12542 Sentence denotes Public health measures should be in place to immediately test and isolate infected persons.
T93 12544-12575 Sentence denotes Quarantine in the wider context
T94 12576-12893 Sentence denotes The lockdown in China with government enforced movement restriction outdoors combined with facility-based case isolation, rigorous contact tracing and quarantine of all contacts, had a substantial impact on interrupting the chain of human-to-human transmission in Wuhan, thus effectively containing the outbreak [16].
T95 12894-13111 Sentence denotes While the outbreak in Wuhan involved a highly urbanised setting, the current lockdown in Italy involves small villages with a different social culture and behaviour, and different mechanisms of quarantine enforcement.
T96 13112-13250 Sentence denotes Our findings suggest that the degree of quarantine adherence needs to be very high regardless of population size in order to be effective.
T97 13251-13386 Sentence denotes We note, however, that a less strict community quarantine could still flatten the curve of the outbreak compared to no quarantine [17].
T98 13387-13540 Sentence denotes In any case, quarantine adherence has an Important and notable impact on reducing the outbreak, but some transmission will still occur within households.
T99 13541-13695 Sentence denotes We showed that in a theoretical scenario of a single-person household with very strict community quarantine measures, no secondary infections would occur.
T100 13696-13947 Sentence denotes While a single-person household does not reflect the reality of any society, it does suggest that if all cases could be isolated, e.g. moved out of the community, the epidemic curve would decline much faster and the lockdown duration could be reduced.
T101 13948-14265 Sentence denotes This means that more efforts need to be done at household level: keeping physical distance even within a household combined with wearing face masks and segregated within-household isolation, or better all symptomatic cases ideally need to be promptly moved out of the household, and isolated in a designated facility.
T102 14266-14346 Sentence denotes Prompt testing is therefore needed for timely diagnosis and immediate isolation.
T103 14347-14466 Sentence denotes We also show that a 14-days lockdown period is not sufficient for most scenarios; a longer lockdown duration is needed.
T104 14467-14600 Sentence denotes On 8 March, Italy announced the need to extend the lockdown to include around 16 million people for 25 additional days until 3 April.
T105 14601-14837 Sentence denotes Such longer duration should in fact be expected to be required, to have a positive impact, which is going to be very challenging for affected communities to be supplied in food, essential services and to be able to cope psychologically.
T106 14838-15058 Sentence denotes If lockdown is enforced, it must be done rigorously to truly interrupt transmission, and this would mean near 100% restriction of contacts between persons within the community combined with prompt isolation of new cases.
T107 15059-15220 Sentence denotes Less strict quarantine adherence would imply even longer lockdown periods, and longer lockdown periods will likely present even greater socioeconomic challenges.
T108 15221-15446 Sentence denotes By implementing the world’s largest lockdown combined with prompt case isolation, contact tracing of contacts and with strict enforcement of physical distancing [16], containment of COVID-19 in China was shown to be feasible.
T109 15447-15748 Sentence denotes Remarkably, in South Korea, the control of the outbreak, which had been temporarily lost, was regained without lockdown but with rigorous active case finding, by liberal testing, prompt isolation, and by using novel digital technologies to maximise contact tracing and quarantine of all contacts [18].
T110 15749-16066 Sentence denotes In certain places like Taiwan [19], Singapore [20] and Hong Kong, a flat epidemic curve was maintained for COVID-19 by applying very liberal testing, prompt case isolation outside of the community (no home isolation even of the mildest cases), and technologically enhanced contact tracing, very early in the outbreak.
T111 16067-16327 Sentence denotes If the lockdown in Italy, and meanwhile in many other European countries, is aimed at containment, close to 100% restriction of contact time within communities combined with prompt case detection and immediate isolation of infected persons need to be achieved.
T112 16329-16350 Sentence denotes Conflict of interest:
T113 16351-16365 Sentence denotes None declared.
T114 16366-16442 Sentence denotes Authors’ contributions: HS and ZF did the modelling and created the figures.
T115 16443-16466 Sentence denotes AWS had the study idea.
T116 16467-16543 Sentence denotes JR, HS and AWS conceptualized the study; AWS, JR and SO provided parameters.
T117 16544-16599 Sentence denotes AWS, HS and JR wrote the first draft of the manuscript.
T118 16600-16648 Sentence denotes All authors contributed to the final manuscript.
T119 16650-16668 Sentence denotes Supplementary Data
T120 16669-16681 Sentence denotes Supplement 1
T121 16682-16718 Sentence denotes Click here for additional data file.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T1 45-56 NCBITaxon:11118 denotes coronavirus
T2 66-74 SP_7 denotes COVID-19
T3 166-174 SP_7 denotes COVID-19
T4 658-669 NCBITaxon:11118 denotes coronavirus
T5 679-687 SP_7 denotes COVID-19
T6 1042-1048 NCBITaxon:9606 denotes people
T7 1212-1223 NCBITaxon:1 denotes individuals
T8 1285-1293 SP_7 denotes COVID-19
T9 1302-1308 GO:0016265 denotes deaths
T10 1523-1530 GO:0065007 denotes control
T11 1758-1769 NCBITaxon:1 denotes individuals
T12 2255-2263 SP_7 denotes COVID-19
T13 2759-2766 NCBITaxon:9606 denotes persons
T14 2786-2793 NCBITaxon:9606 denotes persons
T15 2824-2831 NCBITaxon:1 denotes persons
T16 3119-3126 NCBITaxon:1 denotes Persons
T17 3340-3348 SP_7 denotes COVID-19
T18 3683-3691 SP_7 denotes COVID-19
T19 3693-3704 NCBITaxon:11118 denotes coronavirus
T20 3874-3879 NCBITaxon:10239 denotes virus
T21 3912-3918 NCBITaxon:9606 denotes person
T22 4006-4018 GO:0000003 denotes reproductive
T23 4853-4859 NCBITaxon:9606 denotes person
T24 4987-4998 NCBITaxon:1 denotes individuals
T25 5546-5553 NCBITaxon:1 denotes persons
T26 5593-5600 NCBITaxon:1 denotes persons
T27 5625-5631 NCBITaxon:9606 denotes person
T28 5861-5868 NCBITaxon:1 denotes persons
T29 6158-6165 NCBITaxon:9606 denotes persons
T30 6311-6318 NCBITaxon:1 denotes persons
T31 6597-6605 SP_7 denotes COVID-19
T32 6676-6683 NCBITaxon:1 denotes persons
T33 6815-6823 SP_7 denotes COVID-19
T34 6825-6836 NCBITaxon:11118 denotes coronavirus
T35 6959-6965 NCBITaxon:9606 denotes person
T36 7659-7665 NCBITaxon:9606 denotes person
T37 7787-7793 NCBITaxon:9606 denotes person
T38 8091-8098 NCBITaxon:1 denotes persons
T39 8314-8320 NCBITaxon:9606 denotes person
T40 8476-8482 NCBITaxon:9606 denotes person
T41 8493-8499 NCBITaxon:9606 denotes person
T42 8527-8533 NCBITaxon:9606 denotes person
T43 8917-8923 NCBITaxon:9606 denotes people
T44 8978-8985 NCBITaxon:1 denotes persons
T45 9503-9509 NCBITaxon:9606 denotes person
T46 10178-10186 SP_7 denotes COVID-19
T47 10296-10304 SP_7 denotes COVID-19
T48 10306-10317 NCBITaxon:11118 denotes coronavirus
T49 11737-11745 SP_7 denotes COVID-19
T50 12230-12241 NCBITaxon:1 denotes individuals
T51 12388-12395 NCBITaxon:1 denotes persons
T52 12534-12541 NCBITaxon:1 denotes persons
T53 12809-12814 SP_6;NCBITaxon:9606 denotes human
T54 12818-12823 SP_6;NCBITaxon:9606 denotes human
T55 13594-13600 NCBITaxon:1 denotes person
T56 13711-13717 NCBITaxon:9606 denotes person
T57 14085-14089 UBERON:0001456 denotes face
T58 14556-14562 NCBITaxon:9606 denotes people
T59 14773-14777 CHEBI:33290;CHEBI:33290 denotes food
T60 14985-14992 NCBITaxon:1 denotes persons
T61 15403-15411 SP_7 denotes COVID-19
T62 15479-15486 GO:0065007 denotes control
T63 15856-15864 SP_7 denotes COVID-19
T64 16299-16306 NCBITaxon:1 denotes persons
T23141 45-56 NCBITaxon:11118 denotes coronavirus
T43187 66-74 SP_7 denotes COVID-19
T74064 166-174 SP_7 denotes COVID-19
T70092 658-669 NCBITaxon:11118 denotes coronavirus
T96053 679-687 SP_7 denotes COVID-19
T17081 1042-1048 NCBITaxon:9606 denotes people
T5069 1212-1223 NCBITaxon:1 denotes individuals
T24867 1285-1293 SP_7 denotes COVID-19
T14047 1302-1308 GO:0016265 denotes deaths
T44308 1523-1530 GO:0065007 denotes control
T21705 1758-1769 NCBITaxon:1 denotes individuals
T8747 2255-2263 SP_7 denotes COVID-19
T53876 2759-2766 NCBITaxon:9606 denotes persons
T59333 2786-2793 NCBITaxon:9606 denotes persons
T81704 2824-2831 NCBITaxon:1 denotes persons
T33464 3119-3126 NCBITaxon:1 denotes Persons
T97087 3340-3348 SP_7 denotes COVID-19
T34779 3683-3691 SP_7 denotes COVID-19
T67934 3693-3704 NCBITaxon:11118 denotes coronavirus
T46954 3874-3879 NCBITaxon:10239 denotes virus
T52028 3912-3918 NCBITaxon:9606 denotes person
T34369 4006-4018 GO:0000003 denotes reproductive
T38063 4853-4859 NCBITaxon:9606 denotes person
T85748 4987-4998 NCBITaxon:1 denotes individuals
T20142 5546-5553 NCBITaxon:1 denotes persons
T31054 5593-5600 NCBITaxon:1 denotes persons
T17648 5625-5631 NCBITaxon:9606 denotes person
T71332 5861-5868 NCBITaxon:1 denotes persons
T15041 6158-6165 NCBITaxon:9606 denotes persons
T52416 6311-6318 NCBITaxon:1 denotes persons
T23901 6597-6605 SP_7 denotes COVID-19
T3263 6676-6683 NCBITaxon:1 denotes persons
T72526 6815-6823 SP_7 denotes COVID-19
T31879 6825-6836 NCBITaxon:11118 denotes coronavirus
T18296 6959-6965 NCBITaxon:9606 denotes person
T50843 7659-7665 NCBITaxon:9606 denotes person
T27416 7787-7793 NCBITaxon:9606 denotes person
T17704 8091-8098 NCBITaxon:1 denotes persons
T42718 8314-8320 NCBITaxon:9606 denotes person
T91727 8476-8482 NCBITaxon:9606 denotes person
T20761 8493-8499 NCBITaxon:9606 denotes person
T97626 8527-8533 NCBITaxon:9606 denotes person
T59377 8917-8923 NCBITaxon:9606 denotes people
T3143 8978-8985 NCBITaxon:1 denotes persons
T84616 9503-9509 NCBITaxon:9606 denotes person
T39600 10178-10186 SP_7 denotes COVID-19
T58609 10296-10304 SP_7 denotes COVID-19
T4044 10306-10317 NCBITaxon:11118 denotes coronavirus
T55518 11737-11745 SP_7 denotes COVID-19
T46047 12230-12241 NCBITaxon:1 denotes individuals
T57216 12388-12395 NCBITaxon:1 denotes persons
T81759 12534-12541 NCBITaxon:1 denotes persons
T48606 12809-12814 SP_6;NCBITaxon:9606 denotes human
T14800 12818-12823 SP_6;NCBITaxon:9606 denotes human
T53961 13594-13600 NCBITaxon:1 denotes person
T3270 13711-13717 NCBITaxon:9606 denotes person
T86317 14085-14089 UBERON:0001456 denotes face
T71220 14556-14562 NCBITaxon:9606 denotes people
T92995 14773-14777 CHEBI:33290;CHEBI:33290 denotes food
T64157 14985-14992 NCBITaxon:1 denotes persons
T44545 15403-15411 SP_7 denotes COVID-19
T4478 15479-15486 GO:0065007 denotes control
T61220 15856-15864 SP_7 denotes COVID-19
T31434 16299-16306 NCBITaxon:1 denotes persons

MyTest

Id Subject Object Predicate Lexical cue
32265005-32199470-29326713 814-815 32199470 denotes 1
32265005-24060621-29326714 2203-2204 24060621 denotes 3
32265005-32074444-29326715 2330-2331 32074444 denotes 6
32265005-31995857-29326716 2332-2333 31995857 denotes 7
32265005-32183930-29326717 3113-3114 32183930 denotes 8
32265005-32179137-29326718 3115-3116 32179137 denotes 9
32265005-23665296-29326719 4176-4178 23665296 denotes 10
32265005-23665296-29326720 4311-4313 23665296 denotes 10
32265005-32109273-29326721 4314-4316 32109273 denotes 11
32265005-32227186-29326722 11781-11783 32227186 denotes 13
32265005-32181488-29326723 12889-12891 32181488 denotes 16
32265005-32164834-29326724 13382-13384 32164834 denotes 17
32265005-32181488-29326725 15383-15385 32181488 denotes 16
32265005-32149043-29326726 15744-15746 32149043 denotes 18
32265005-32125371-29326727 15780-15782 32125371 denotes 19
32265005-32167146-29326728 15796-15798 32167146 denotes 20