> top > docs > PMC:7738161 > spans > 7155-12869 > annotations

PMC:7738161 / 7155-12869 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
57 570-578 Species denotes patients Tax:9606
58 651-657 Species denotes people Tax:9606
59 66-82 Disease denotes British Columbia OMIM:176500
60 703-723 Disease denotes respiratory symptoms MESH:D012818
61 1002-1010 Disease denotes infected MESH:D007239
63 1263-1279 Disease denotes British Columbia OMIM:176500
67 1715-1717 Chemical denotes ur MESH:D014529
68 1719-1721 Chemical denotes ur MESH:D014529
69 1724-1726 Chemical denotes ud
72 2319-2325 Species denotes people Tax:9606
73 2381-2387 Species denotes people Tax:9606
75 3692-3697 Disease denotes COVID MESH:C000657245
77 5245-5253 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T46 0-4 Sentence denotes Data
T47 5-228 Sentence denotes We fit the physical distancing model to case-count data from British Columbia from March 1, 2020 (when a total of eight cases had been detected in the province) to April 11, 2020 at which time 1445 cases had been confirmed.
T48 229-418 Sentence denotes These data are available in press releases from the BC Centre for Disease Control (BCCDC) [10], from the public data dashboard [17], and from the code repository associated with this paper.
T49 419-483 Sentence denotes Testing procedures were adapted over the course of the outbreak.
T50 484-724 Sentence denotes In particular, lab testing criteria were changed on March 16 to focus on hospitalized patients, healthcare workers, long-term care facility residents/staff, and those people part of an existing cluster and experiencing respiratory symptoms.
T51 725-849 Sentence denotes This led to high variability in case counts in the surrounding days with some large jumps in the number of identified cases.
T52 850-1046 Sentence denotes We accounted for this in the model by adjusting the testing fraction ψr to accommodate widening the testing pool and thereby increasing the fraction of infected individuals being tested (Table 1).
T53 1047-1100 Sentence denotes There was also variability in the daily testing rate.
T54 1101-1230 Sentence denotes During March, the daily number of completed tests ranged from approximately 100 to 3500, and did not strictly increase over time.
T55 1231-1384 Sentence denotes Table 1 Values and sources for British Columbia parameterization of the model (see Supplemental Methods and Table B in S1 Text for other jurisdictions).
T56 1385-1527 Sentence denotes The duration of the infectious period is shorter than the duration of severe illness, accounting for self-isolation and less severe illnesses.
T57 1528-1677 Sentence denotes The quarantine parameter q reflects approximately 1/5 of severe cases either ceasing to transmit due to hospitalization or completely self-isolating.
T58 1678-1817 Sentence denotes The model depends on the combination ur/(ur + ud), the fraction engaged in physical distancing, estimated from the survey data cited above.
T59 1818-1969 Sentence denotes The testing patterns have changed over time, with laboratories increasing the numbers of tests on approximately March 14 (motivating our change in ψr).
T60 1970-2027 Sentence denotes Symbol Definition Specified/fitted value Justification
T61 2028-2063 Sentence denotes N Population size 5,100,000 [23]
T62 2064-2123 Sentence denotes D Mean duration of the infectious period 5 days [24, 25]
T63 2124-2187 Sentence denotes k 1 (time to infectiousness)−1 (E1 to E2) 0.2 days−1 [26–28]
T64 2188-2274 Sentence denotes k 2 (time period of pre-symptomatic transmissibility)−1 (E2 to I) 1 days−1 [27, 28]
T65 2275-2305 Sentence denotes q Quarantine rate 0.05 [29]
T66 2306-2366 Sentence denotes u d Rate of people moving to physical distancing 0.1 [20]
T67 2367-2434 Sentence denotes u r Rate of people returning from physical distancing 0.02 [20]
T68 2435-2532 Sentence denotes ψ r Proportion of anticipated cases on day r that are tested and reported 0.1 Before March 14
T69 2533-2559 Sentence denotes 0.3 On and after March 14
T70 2560-2669 Sentence denotes Shape Weibull parameter in delay-to-reporting distribution 1.73 (1.60–1.86 95% CI) Fit to data from Fig 1B
T71 2670-2780 Sentence denotes Scale Weibull parameter in delay-to-reporting distribution 9.85 (9.30–10.46 95% CI) Fit to data from Fig 1B
T72 2781-2862 Sentence denotes R 0b Basic reproductive number 2.95 (2.88–3.02 95% CI) Fit to data from Fig 1C
T73 2863-2973 Sentence denotes f 2 Fraction of normal contacts during physical distancing 0.22 (0.08– 0.36 95% CI) Fit to data from Fig 1C
T74 2974-3187 Sentence denotes ϕ Inverse dispersion from negative binomial (NB2) observation model 6.86 (3.39–12.37 95% CI) Fit to data from Fig 1C For some confirmed cases in BC, estimates of the date of symptom onset are available (Fig 1).
T75 3188-3300 Sentence denotes We used the delays between symptom onset and cases being reported to parameterize the physical distancing model.
T76 3301-3443 Sentence denotes In this case-specific data set there were only seven cases reported before February 29, and a decline in reported cases after April 2 (Fig 1).
T77 3444-3590 Sentence denotes Therefore we used only the 535 cases in the case-specific data that were reported between these dates to parameterize the delay part of the model.
T78 3591-3785 Sentence denotes For California (CA), New York (NY), and Florida (FL) we used reported case and testing data from The COVID Tracking Project, and assumed a BC-like delay between symptom onset and case reporting.
T79 3786-3873 Sentence denotes For New Zealand (NZ) we used reported cases from the NZ Ministry of Health [18], and A.
T80 3874-3887 Sentence denotes Lustig and M.
T81 3888-4067 Sentence denotes Plank (pers. comm.) fit the delay distribution to NZ case-reporting data using our package [19], since these data are not publicly available (see Supplemental Methods in S1 Text).
T82 4068-4145 Sentence denotes For our main analysis with BC, we fit our model to data until April 11, 2020.
T83 4146-4389 Sentence denotes When demonstrating the application of our model to other jurisdictions, we included data until May 6 or 7, 2020, the date we completed this portion of the analysis and before these jurisdictions had begun relaxing physical distancing measures.
T84 4390-4679 Sentence denotes An outbreak at a poultry plant in BC, combined with an expansion of testing in mid April, meant that in order to extend the BC model to May 6 or 7, we would have had to introduce changes to the methodology that would not be straightforward and would not be possible in other jurisdictions.
T85 4680-4877 Sentence denotes These include, for example, modelling the poultry workforce’s interventions and contacts and the links between the outbreak and general community transmission, in concert with differential testing.
T86 4878-4942 Sentence denotes We therefore limited the data used for the BC model to April 11.
T87 4943-5147 Sentence denotes We motivated the structure of our model based on a survey conducted by the Angus Reid Institute to examine how physical distancing measures changed behaviour in Canada (March 20–23, 2020; n = 1664; [20]).
T88 5148-5349 Sentence denotes Responses indicated that there was a subset of the population believing that the response to the COVID-19 epidemic was “overblown”, who were less willing than others to engage in distancing behaviours.
T89 5350-5528 Sentence denotes This motivated treating the distancing and non-distancing compartments of our model separately and assuming that ∼80% of individuals were able and willing to physically distance.
T90 5529-5714 Sentence denotes We used the timing of known government interventions to inform the timing of behavioural changes, and verified these dates against publicly available mobility data for each region [21].