> top > projects > LitCovid-sentences > docs > PMC:7001239 > annotations
LitCovid-sentences  

PMC:7001239 JSONTXT 23 Projects

Annnotations TAB TSV DIC JSON TextAE

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.