LitCovid-sentences  

PMC:7001239 / 3291-6257 JSONTXT 11 Projects

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Id Subject Object Predicate Lexical cue
T23 0-38 Sentence denotes Simulating early outbreak trajectories
T24 39-103 Sentence denotes In a first step, we initialised simulations with one index case.
T25 104-248 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 249-480 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 481-622 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 623-751 Sentence denotes We explored a wide range of parameter combinations (Table) and ran 1,000 stochastic simulations for each individual combination.
T29 752-955 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 956-1082 Sentence denotes Table Parameter ranges for stochastic simulations of outbreak trajectories, 2019 novel coronavirus outbreak, China, 2019–2020
T31 1083-1156 Sentence denotes Parameter Description Range Number of values explored within the range
T32 1157-1213 Sentence denotes R0 Basic reproduction number 0.8–5.0 22 (equidistant)
T33 1214-1278 Sentence denotes k Dispersion parameter 0.0110 20 (equidistant on log10 scale)
T34 1279-1345 Sentence denotes D Generation time interval (days) 9–11,13,16–19 8 (equidistant)
T35 1346-1401 Sentence denotes n Initial number of index cases 1–50 6 (equidistant)
T36 1402-1671 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 1672-1804 Sentence denotes An epidemic with several index cases can be considered as the aggregation of several independent epidemics with one index case each.
T38 1805-1958 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 1959-2135 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 2136-2348 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 2349-2555 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 2556-2811 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 2812-2907 Sentence denotes Model simulations and analyses were performed in the R software for statistical computing [11].
T44 2908-2966 Sentence denotes Code files are available on https://github.com/jriou/wcov.