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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
20 22-39 Species denotes novel coronavirus Tax:2697049
21 41-50 Species denotes 2019-nCoV Tax:2697049
22 309-361 Species denotes severe acute respiratory syndrome (SARS) coronavirus Tax:694009
23 366-417 Species denotes Middle East respiratory syndrome (MERS) coronavirus Tax:1335626
24 1154-1163 Species denotes 2019-nCoV Tax:2697049
25 1245-1258 Species denotes coronaviruses Tax:11118
26 114-129 Disease denotes viral pneumonia
27 257-289 Disease denotes severe acute respiratory disease MESH:D045169
28 1232-1236 Disease denotes SARS MESH:D045169
29 1240-1244 Disease denotes MERS MESH:D018352
31 1366-1385 Disease denotes 2019-nCoV infection MESH:C000657245
33 1516-1548 Disease denotes 2019 novel coronavirus infection MESH:C000657245
38 1683-1692 Species denotes 2019-nCoV Tax:2697049
39 1669-1677 Disease denotes infected MESH:D007239
40 2059-2067 Disease denotes infected MESH:D007239
41 2162-2171 Disease denotes infection MESH:D007239
43 3537-3546 Disease denotes infection MESH:D007239
45 3895-3904 Disease denotes infection MESH:D007239
48 4091-4113 Species denotes 2019 novel coronavirus Tax:2697049
49 4115-4124 Species denotes 2019-nCoV Tax:2697049
52 4272-4280 Disease denotes infected MESH:D007239
53 4348-4357 Disease denotes infection MESH:D007239
57 5090-5112 Species denotes 2019 novel coronavirus Tax:2697049
58 5114-5123 Species denotes 2019-nCoV Tax:2697049
59 5076-5084 Disease denotes infected MESH:D007239
63 5776-5798 Species denotes 2019 novel coronavirus Tax:2697049
64 5800-5809 Species denotes 2019-nCoV Tax:2697049
65 5762-5770 Disease denotes infected MESH:D007239
69 6534-6556 Species denotes 2019 novel coronavirus Tax:2697049
70 6558-6567 Species denotes 2019-nCoV Tax:2697049
71 6516-6524 Disease denotes infected MESH:D007239
76 6739-6761 Species denotes 2019 novel coronavirus Tax:2697049
77 6834-6847 Species denotes coronaviruses Tax:11118
78 6763-6796 Disease denotes severe acute respiratory syndrome MESH:D045169
79 6801-6833 Disease denotes Middle East respiratory syndrome MESH:D018352
85 7261-7270 Species denotes 2019-nCoV Tax:2697049
86 6933-6937 Disease denotes MERS MESH:D018352
87 7155-7159 Disease denotes SARS MESH:D045169
88 7392-7396 Disease denotes MERS MESH:D018352
89 7400-7404 Disease denotes SARS MESH:D045169
103 7683-7692 Species denotes 2019-nCoV Tax:2697049
104 7744-7753 Species denotes 2019-nCoV Tax:2697049
105 7803-7812 Species denotes 2019-nCoV Tax:2697049
106 7878-7882 Disease denotes SARS MESH:D045169
107 7934-7938 Disease denotes SARS MESH:D045169
108 7997-8001 Disease denotes SARS MESH:D045169
109 8060-8064 Disease denotes SARS MESH:D045169
110 8121-8125 Disease denotes SARS MESH:D045169
111 8185-8189 Disease denotes SARS MESH:D045169
112 8251-8255 Disease denotes MERS MESH:D018352
113 8321-8325 Disease denotes MERS MESH:D018352
114 8385-8389 Disease denotes MERS MESH:D018352
115 8464-8468 Disease denotes MERS MESH:D018352
117 7525-7538 Species denotes coronaviruses Tax:11118
124 8567-8576 Species denotes 2019-nCoV Tax:2697049
125 8578-8600 Species denotes 2019 novel coronavirus Tax:2697049
126 8602-8606 Disease denotes SARS MESH:D045169
127 8608-8641 Disease denotes severe acute respiratory syndrome MESH:D045169
128 8667-8671 Disease denotes MERS MESH:D018352
129 8673-8705 Disease denotes Middle East respiratory syndrome MESH:D018352
131 8966-8979 Species denotes coronaviruses Tax:11118
138 9003-9012 Species denotes 2019-nCoV Tax:2697049
139 9014-9036 Species denotes 2019 novel coronavirus Tax:2697049
140 9038-9042 Disease denotes SARS MESH:D045169
141 9044-9077 Disease denotes severe acute respiratory syndrome MESH:D045169
142 9079-9083 Disease denotes MERS MESH:D018352
143 9085-9117 Disease denotes Middle East respiratory syndrome MESH:D018352
147 9337-9346 Species denotes 2019-nCoV Tax:2697049
148 9323-9331 Disease denotes infected MESH:D007239
149 9573-9577 Disease denotes fits MESH:D012640
152 10286-10294 Disease denotes infected MESH:D007239
153 10429-10437 Disease denotes infected MESH:D007239
156 11181-11190 Species denotes 2019-nCoV Tax:2697049
157 11249-11254 Species denotes women Tax:9606

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 9456-9460 Body_part denotes back http://purl.org/sig/ont/fma/fma25056

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T4 74-84 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T5 114-129 Disease denotes viral pneumonia http://purl.obolibrary.org/obo/MONDO_0006012
T6 120-129 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T7 270-289 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T8 309-342 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T9 344-348 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 1232-1236 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T11 1366-1385 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T12 1376-1385 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 1516-1548 Disease denotes 2019 novel coronavirus infection http://purl.obolibrary.org/obo/MONDO_0100096
T14 1539-1548 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 2162-2171 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T16 3537-3546 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T17 3895-3904 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 4348-4357 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T19 6763-6796 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T20 7155-7159 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T21 7400-7404 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T22 7878-7882 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 7934-7938 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T24 7997-8001 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T25 8060-8064 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T26 8121-8125 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T27 8185-8189 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T28 8572-8582 Disease denotes nCoV: 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T29 8602-8606 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T30 8608-8641 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T31 9008-9018 Disease denotes nCoV: 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T32 9038-9042 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 9044-9077 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 20-21 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 237-242 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 534-539 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 1085-1088 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3-5
T6 1946-1952 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T7 1965-1969 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T8 1965-1969 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T9 2311-2312 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2492-2495 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T11 2686-2688 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T12 2799-2800 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 3044-3045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 3286-3288 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T15 3286-3288 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T16 3451-3452 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3582-3591 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T18 3811-3812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4007-4008 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 4717-4718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 4764-4765 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 4979-4980 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 5534-5535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 5536-5545 http://purl.obolibrary.org/obo/UBERON_0001353 denotes Posterior
T25 5554-5555 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T26 5622-5623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 6383-6384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 6385-6394 http://purl.obolibrary.org/obo/UBERON_0001353 denotes Posterior
T29 6610-6619 http://purl.obolibrary.org/obo/UBERON_0001353 denotes Posterior
T30 6868-6869 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T31 7444-7445 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 7569-7574 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T33 8180-8182 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T34 8707-8708 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 8773-8774 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T36 9472-9473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 9697-9699 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T38 9829-9831 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T39 9940-9943 http://purl.obolibrary.org/obo/CLO_0001577 denotes a 3
T40 10031-10032 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 10066-10067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 10249-10250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 10514-10515 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 10678-10679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 10757-10761 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T46 10757-10761 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T47 10971-10972 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 11038-11039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 11687-11688 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1965-1969 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T2 2985-2990 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T3 3286-3288 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T4 3717-3719 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T5 4690-4695 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T6 5263-5265 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T7 5510-5512 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T8 7911-7913 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T9 7981-7984 Chemical denotes Lau http://purl.obolibrary.org/obo/CHEBI_32359
T10 8031-8033 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T11 8041-8043 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T12 8044-8047 Chemical denotes Lau http://purl.obolibrary.org/obo/CHEBI_32359
T13 8092-8094 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T14 8102-8104 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T15 8105-8108 Chemical denotes Lau http://purl.obolibrary.org/obo/CHEBI_32359
T16 8152-8154 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T17 8162-8164 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T18 8360-8362 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T19 8548-8550 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T20 8643-8645 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T21 8872-8874 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T22 10757-10761 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T23 11745-11750 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T7 0-214 Sentence denotes Early January 2020, a novel coronavirus (2019-nCoV) was identified as the infectious agent causing an outbreak of viral pneumonia in Wuhan, China, where the first cases had their symptom onset in December 2019 [1].
T8 215-455 Sentence denotes This newly discovered virus, which causes severe acute respiratory disease, is related to the severe acute respiratory syndrome (SARS) coronavirus and Middle East respiratory syndrome (MERS) coronavirus, but distinct from each of these [2].
T9 456-629 Sentence denotes The key epidemiological parameters, including incubation period, for this new virus are therefore rapidly being studied from incoming case reports as the epidemic continues.
T10 630-701 Sentence denotes Chief among these key parameters is the incubation period distribution.
T11 702-870 Sentence denotes The range of the values for the incubation period is essential to epidemiological case definitions, and is required to determine the appropriate duration of quarantine.
T12 871-989 Sentence denotes Moreover, knowledge of the incubation period helps to assess the effectiveness of entry screening and contact tracing.
T13 990-1127 Sentence denotes The distribution of the incubation period is also used in estimating the size of the epidemic [3-5] and the transmission potential [6,7].
T14 1128-1259 Sentence denotes In absence of data on the 2019-nCoV incubation period, these studies have assumed incubation periods of SARS or MERS coronaviruses.
T15 1260-1477 Sentence denotes Here we present the distribution of incubation periods estimated for travellers from Wuhan with confirmed 2019-nCoV infection in the early outbreak phase, using their reported travel histories and symptom onset dates.
T16 1479-1605 Sentence denotes Travellers from Wuhan with confirmed 2019 novel coronavirus infection, reported symptom onset data and reported travel history
T17 1606-1721 Sentence denotes In January 2020, an increasing number of cases confirmed to be infected with 2019-nCoV were detected outside Wuhan.
T18 1722-1856 Sentence denotes For 88 cases detected between 20 and 28 January, the travel history (to and) from Wuhan is known, as well as their symptom onset date.
T19 1857-1970 Sentence denotes Their ages range from 2 to 72 years of age (information missing for four cases); 31 were female and 57 were male.
T20 1971-2077 Sentence denotes During this initial stage of the epidemic, it is most likely that these travellers were infected in Wuhan.
T21 2078-2172 Sentence denotes Consequently, their time spent in Wuhan can be taken as the duration of exposure to infection.
T22 2173-2326 Sentence denotes Of these 88 cases with known travel history, 63 were Wuhan residents who travelled elsewhere and 25 were visitors who stayed in Wuhan for a limited time.
T23 2327-2459 Sentence denotes By taking the date of symptom onset and travel history together, we inferred the possible incubation period for each of these cases.
T24 2460-2612 Sentence denotes The data used for this analysis has been translated from Chinese sources such as provincial centres of disease control, and made publicly available [8].
T25 2613-2690 Sentence denotes We took the data as available on 29 January 2020 (Supplementary Material S1).
T26 2692-2722 Sentence denotes Incubation period distribution
T27 2723-2865 Sentence denotes Using the duration of stay in Wuhan and the symptom onset date, we obtained a range of possible values for the incubation period of each case.
T28 2866-3035 Sentence denotes We fitted three parametric forms for the incubation period distribution to these ranges: the Weibull distribution, the gamma distribution and the lognormal distribution.
T29 3036-3141 Sentence denotes We used a Bayesian approach to fitting that allows for the use of prior knowledge to inform the analysis.
T30 3142-3336 Sentence denotes We specified strictly positive flat prior probability distributions for the parameter values of the three distributions (Supplementary Material S2), which ensured our estimates are conservative.
T31 3337-3442 Sentence denotes Because of the sufficient number of observations, the impact of the priors on the outcome was negligible.
T32 3443-3561 Sentence denotes We used a uniform prior probability distribution over the exposure interval for the moment of infection for each case.
T33 3562-3721 Sentence denotes We sampled from the posterior distribution using the rstan package [9] in R software version 3.6.0 (R Foundation, Vienna, Austria) (Supplementary Material S3).
T34 3722-3871 Sentence denotes Figure 1 shows the exposure to reporting timeline for each case, where the cases without a maximum incubation period lack an unexposed (grey) period.
T35 3872-4035 Sentence denotes However, the estimated infection times for these cases are close to the end of the exposure window, informed by the cases that do have a maximum incubation period.
T36 4036-4226 Sentence denotes Figure 1 Exposure to reporting timeline for confirmed 2019 novel coronavirus (2019-nCoV) cases with travel history from Wuhan, sorted by symptom onset date, data 20–28 January 2020 (n = 88)
T37 4227-4398 Sentence denotes The analysis yields the probability of being infected (dark pink), i.e. the cumulative density function of the estimated infection moments, using the Weibull distribution.
T38 4399-4468 Sentence denotes The Weibull distribution provided the best fit to the data (Table 1).
T39 4469-4553 Sentence denotes The mean incubation period was estimated to be 6.4 days (95% credible interval (CI):
T40 4554-4563 Sentence denotes 5.6–7.7).
T41 4564-4667 Sentence denotes The incubation period ranges from 2.1 to 11.1 days (2.5th to 97.5th percentile) (Table 2 and Figure 2).
T42 4668-4803 Sentence denotes The results using the gamma distribution provide a slightly poorer description of the data, but a similar range: from 2.4 to 12.5 days.
T43 4804-5023 Sentence denotes Although the lognormal distribution provides the poorest fit to the data, the incubation period ranging from 2.4 to 15.5 days (2.5th to 97.5th percentile) may be relevant for a conservative choice of quarantine periods.
T44 5024-5235 Sentence denotes Table 1 Estimated incubation period for travellers infected with 2019 novel coronavirus (2019-nCoV) in Wuhan, China, for different parametric forms of the incubation period distribution, data 20–28 January 2020
T45 5236-5281 Sentence denotes Distribution Mean (days) SD (days) LOO ICb
T46 5282-5318 Sentence denotes Estimatea 95% CI Estimatea 95% CI
T47 5319-5359 Sentence denotes Weibull 6.4 5.6–7.7 2.3 1.7–3.7 486
T48 5360-5398 Sentence denotes Gamma 6.5 5.6–7.9 2.6 1.8–4.2 545
T49 5399-5441 Sentence denotes Lognormal 6.8 5.7–8.8 3.4 2.1–6.4 592
T50 5442-5472 Sentence denotes CI: credible interval; LOO IC:
T51 5473-5533 Sentence denotes Leave-one-out information criterion; SD: standard deviation.
T52 5534-5553 Sentence denotes a Posterior median.
T53 5554-5694 Sentence denotes b LOO IC indicates the goodness-of-fit, where lower values indicate a better fit and differences larger than two are statistically relevant.
T54 5695-5921 Sentence denotes Table 2 Percentiles of estimated incubation period for travellers infected with 2019 novel coronavirus (2019-nCoV) in Wuhan, China, for different parametric forms of the incubation period distribution, data 20–28 January 2020
T55 5922-5972 Sentence denotes Percentiles Incubation period distribution (days)
T56 5973-5998 Sentence denotes Weibull Gamma Lognormal
T57 5999-6054 Sentence denotes Estimatea 95% CI Estimatea 95% CI Estimatea 95% CI
T58 6055-6102 Sentence denotes 2.5th 2.1 1.3–3.0 2.4 1.5–3.2 2.4 1.6–3.1
T59 6103-6148 Sentence denotes 5th 2.7 1.8–3.5 2.9 2.0–3.6 2.8 2.0–3.5
T60 6149-6195 Sentence denotes 50th 6.4 5.5–7.5 6.1 5.3–7.3 6.1 5.2–7.4
T61 6196-6248 Sentence denotes 95th 10.3 8.6–14.1 11.3 9.1–15.7 13.3 9.9–20.5
T62 6249-6304 Sentence denotes 97.5th 11.1 9.1–15.5 12.5 9.9–17.9 15.5 11.0–25.2
T63 6305-6359 Sentence denotes 99th 11.9 9.7–17.2 14.1 10.9–20.6 18.5 12.6–32.2
T64 6360-6382 Sentence denotes CI: credible interval.
T65 6383-6402 Sentence denotes a Posterior median.
T66 6403-6609 Sentence denotes Figure 2 The cumulative density function of the estimated Weibull incubation period distribution for travellers infected with the 2019 novel coronavirus (2019-nCoV) in Wuhan, China, data 20–28 January 2020
T67 6610-6723 Sentence denotes Posterior median of mean is indicated by the dark blue line and the 95% credible interval by the light blue area.
T68 6725-6867 Sentence denotes Comparison of 2019 novel coronavirus, severe acute respiratory syndrome and Middle East respiratory syndrome coronaviruses’ incubation periods
T69 6868-7112 Sentence denotes A comparison to the estimated incubation period distribution for MERS (Table 3 and Figure 3) shows that the incubation period values are remarkably similar, with mean values differing at most 1 day and 95th percentiles differing at most 2 days.
T70 7113-7271 Sentence denotes The estimated mean incubation periods for SARS are more variable between studies, including values shorter and longer than those presented here for 2019-nCoV.
T71 7272-7482 Sentence denotes These findings imply that the findings of previous studies that have assumed incubation period distributions similar to MERS or SARS will not have to be adapted because of a shorter or longer incubation period.
T72 7483-7561 Sentence denotes Table 3 Estimated incubation periods for coronaviruses from different studies
T73 7562-7635 Sentence denotes Study Virus(location) Distribution Mean (days) 95th percentile (days)
T74 7636-7670 Sentence denotes Estimate 95% CI Estimate 95% CI
T75 7671-7731 Sentence denotes This study 2019-nCoV Weibull 6.4 5.6–7.7 10.3 8.6–14.1
T76 7732-7790 Sentence denotes This study 2019-nCoV Gamma 6.5 5.6–7.9 11.3 9.1–15.7
T77 7791-7853 Sentence denotes This study 2019-nCoV Lognormal 6.8 5.7–8.8 13.3 9.9–20.5
T78 7854-7913 Sentence denotes Donnelly, 2003 [14,15] SARS Gamma 3.8 3.0–4.9 9.45 NA
T79 7914-7980 Sentence denotes Cowling, 2007 [16] SARS Lognormal 5.1 4.6–5.5 12.9 11.7–14.5
T80 7981-8043 Sentence denotes Lau, 2010 [17] SARS (Hong Kong) Lognormal 4.4 NA 12.4 NA
T81 8044-8104 Sentence denotes Lau, 2010 [17] SARS (Beijing) Lognormal 5.7 NA 19.7 NA
T82 8105-8164 Sentence denotes Lau, 2010 [17] SARS (Taiwan) Lognormal 6.9 NA 17.9 NA
T83 8165-8231 Sentence denotes Lessler, 2009 [18] SARS Lognormal 4.8a 3.6–4.4 10.6 8.9–12.2
T84 8232-8298 Sentence denotes Assiri, 2013 [19] MERS Lognormal 6.0b 1.9–14.7 12.4 7.3–17.5
T85 8299-8362 Sentence denotes Cauchemez, 2014 [20] MERS Lognormal 5.5 3.6–10.2 10.2c NA
T86 8363-8441 Sentence denotes Virlogeux, 2016 [21] MERS (South Korea) Gamma 6.9 6.3–7.5 12.7 11.5–14.4
T87 8442-8524 Sentence denotes Virlogeux, 2016 [21] MERS (Saudi Arabia) Lognormal 5.0 4.0–6.6 11.4 8.5–17.5
T88 8525-8577 Sentence denotes CI: credible interval; NA: not available; 2019-nCoV:
T89 8578-8672 Sentence denotes 2019 novel coronavirus; SARS; severe acute respiratory syndrome; SD: standard deviation; MERS:
T90 8673-8706 Sentence denotes Middle East respiratory syndrome.
T91 8707-8772 Sentence denotes a Value calculated from median of 4.0 days provided in reference.
T92 8773-8838 Sentence denotes b Value calculated from median of 5.2 days provided in reference.
T93 8839-8897 Sentence denotes c Value calculated from mean and SD provided in reference.
T94 8898-9002 Sentence denotes Figure 3 Box-and-whisker-plots of estimated incubation periods for coronaviruses from different studies
T95 9003-9013 Sentence denotes 2019-nCoV:
T96 9014-9084 Sentence denotes 2019 novel coronavirus; SARS; severe acute respiratory syndrome; MERS:
T97 9085-9118 Sentence denotes Middle East respiratory syndrome.
T98 9119-9228 Sentence denotes Median (black point), interquartile range (box), and maximum of 1.5 times the interquartile range (whiskers).
T99 9230-9240 Sentence denotes Discussion
T100 9241-9414 Sentence denotes We characterised the distribution of incubation periods for travellers from Wuhan infected with 2019-nCoV in Wuhan who were reported as cases between 20 and 28 January 2020.
T101 9415-9701 Sentence denotes The study provides empirical evidence to back reports on a familial cluster where five family members developed symptoms 3 to 6 days after exposure [10], and fits within the range for the incubation period of 0 to 14 days assumed by the WHO and of 2 to 12 days assumed by the ECDC [11].
T102 9702-9826 Sentence denotes Our estimate of the mean incubation period is longer than the value of 5.2 days based on 10 cases [12], and 4.8 days (range:
T103 9827-9889 Sentence denotes 2–11) based on 16 travellers between Wuhan and Guangdong [13].
T104 9890-9964 Sentence denotes The latter study is restricted to travellers with a 3-day exposure window.
T105 9965-10107 Sentence denotes Repeating our analysis with only the 25 visitors to Wuhan who had a closed exposure window, leads to a mean incubation period of 4.5 days (CI:
T106 10108-10209 Sentence denotes 3.7–5.6) which is more in line with the studies above, but the 95th percentile drops to 8.0 days (CI:
T107 10210-10220 Sentence denotes 6.3–11.8).
T108 10221-10330 Sentence denotes In our analysis, we assumed a uniform prior probability of being infected during the period of stay in Wuhan.
T109 10331-10494 Sentence denotes Since the epidemic was developing during that time period, it is more likely that travellers were infected towards the end rather than the beginning of their stay.
T110 10495-10638 Sentence denotes This might produce a slight bias towards longer incubation periods, so the estimated upper limit of 11.1 days could be considered conservative.
T111 10639-10719 Sentence denotes The travellers in this study represent a selective sample of the reported cases.
T112 10720-10806 Sentence denotes We found travellers to be more often male and younger than the cases reported in [12].
T113 10807-10901 Sentence denotes The numbers are too small to detect systematic differences in incubation time with age or sex.
T114 10902-11075 Sentence denotes Because we only have information on confirmed cases, there is likely a bias towards more severe cases in areas with early awareness and a well-functioning healthcare system.
T115 11076-11281 Sentence denotes As the epidemic continues, it remains important to collect more information on the incubation periods of 2019-nCoV cases with older ages, with underlying morbidity, who are women or who have mild symptoms.
T116 11282-11385 Sentence denotes There are various choices one can make about the parametric form of the incubation period distribution.
T117 11386-11534 Sentence denotes The results with the three often-used forms we report here suggest that there is little impact on the mean and dispersion of the incubation periods.
T118 11535-11636 Sentence denotes Of these three, the lognormal distribution assigns higher probabilities to longer incubation periods.
T119 11637-11877 Sentence denotes Although we found that this distribution provided a poorer description of the data than the Weibull and the gamma distributions, it is prudent not to dismiss the possibility of incubation periods up to 14 days at this stage of the epidemic.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 120-129 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T42 7525-7538 NCBITaxon:11118 denotes coronaviruses
T41 8966-8979 NCBITaxon:11118 denotes coronaviruses
T40 5787-5798 NCBITaxon:11118 denotes coronavirus
T39 5800-5809 SP_7 denotes 2019-nCoV
T38 5101-5112 NCBITaxon:11118 denotes coronavirus
T37 5114-5123 SP_7 denotes 2019-nCoV
T36 6545-6556 NCBITaxon:11118 denotes coronavirus
T35 6558-6567 SP_7 denotes 2019-nCoV
T34 4102-4113 NCBITaxon:11118 denotes coronavirus
T33 4115-4124 SP_7 denotes 2019-nCoV
T32 9337-9346 SP_7 denotes 2019-nCoV
T31 9456-9460 UBERON:0001137 denotes back
T30 11181-11190 SP_7 denotes 2019-nCoV
T29 6933-6937 SP_9 denotes MERS
T28 7155-7159 SP_10 denotes SARS
T27 7261-7270 SP_7 denotes 2019-nCoV
T26 7392-7396 SP_9 denotes MERS
T25 7400-7404 SP_10 denotes SARS
T24 1683-1692 SP_7 denotes 2019-nCoV
T23 28-39 NCBITaxon:11118 denotes coronavirus
T22 41-50 SP_7 denotes 2019-nCoV
T21 114-119 NCBITaxon:10239 denotes viral
T20 237-242 NCBITaxon:10239 denotes virus
T19 270-281 UBERON:0001004 denotes respiratory
T18 322-333 UBERON:0001004 denotes respiratory
T17 344-348 SP_10 denotes SARS
T16 350-361 NCBITaxon:11118 denotes coronavirus
T15 378-389 UBERON:0001004 denotes respiratory
T14 400-404 SP_9;NCBITaxon:10090 denotes MERS
T13 406-417 NCBITaxon:11118 denotes coronavirus
T12 534-539 NCBITaxon:10239 denotes virus
T11 1154-1163 SP_7 denotes 2019-nCoV
T10 1232-1236 SP_10 denotes SARS
T9 1240-1244 SP_9;NCBITaxon:8088 denotes MERS
T8 1245-1258 NCBITaxon:11118 denotes coronaviruses
T7 1366-1375 SP_7 denotes 2019-nCoV

2_test

Id Subject Object Predicate Lexical cue
32046819-12781533-29333935 7870-7872 12781533 denotes 14
32046819-17235210-29333936 7929-7931 17235210 denotes 16
32046819-20205928-29333937 7992-7994 20205928 denotes 17
32046819-20205928-29333938 8055-8057 20205928 denotes 17
32046819-20205928-29333939 8116-8118 20205928 denotes 17
32046819-19393959-29333940 8180-8182 19393959 denotes 18
32046819-23782161-29333941 8246-8248 23782161 denotes 19
32046819-24239323-29333942 8316-8318 24239323 denotes 20
32046819-27775012-29333943 8380-8382 27775012 denotes 21
32046819-27775012-29333944 8459-8461 27775012 denotes 21
32046819-31986261-29333945 9564-9566 31986261 denotes 10
32046819-31995857-29333946 9801-9803 31995857 denotes 12
32046819-31995857-29333947 10802-10804 31995857 denotes 12

MyTest

Id Subject Object Predicate Lexical cue
32046819-12781533-29333935 7870-7872 12781533 denotes 14
32046819-17235210-29333936 7929-7931 17235210 denotes 16
32046819-20205928-29333937 7992-7994 20205928 denotes 17
32046819-20205928-29333938 8055-8057 20205928 denotes 17
32046819-20205928-29333939 8116-8118 20205928 denotes 17
32046819-19393959-29333940 8180-8182 19393959 denotes 18
32046819-23782161-29333941 8246-8248 23782161 denotes 19
32046819-24239323-29333942 8316-8318 24239323 denotes 20
32046819-27775012-29333943 8380-8382 27775012 denotes 21
32046819-27775012-29333944 8459-8461 27775012 denotes 21
32046819-31986261-29333945 9564-9566 31986261 denotes 10
32046819-31995857-29333946 9801-9803 31995857 denotes 12
32046819-31995857-29333947 10802-10804 31995857 denotes 12