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A Time Delay Dynamical Model for Outbreak of 2019-nCoV and the Parameter Identification

Yu Chen, Jin Cheng, Yu Jiang, Keji Liu

arXiv:2002.00418v3q-bio.PEmath.DSphysics.soc-ph

TL;DR

Because 2019-nCoV can spread during its latent period, the paper describes classical SIR, SEIR, and SEIJR models as unsuitable for this outbreak. It proposes a time-delay system using accumulated case counts and reports that isolation rate 0.5 could end the outbreak in around 50 days.

  • Problem

    Because 2019-nCoV can spread during its latent period, the paper describes classical SIR, SEIR, and SEIJR models as unsuitable for the outbreak.

    Source: §1 · p. 2
  • Method

    The proposed time-delay dynamic system uses accumulated population counts as variables and incorporates latent-period spread through the delay process.

    Source: §1 · p. 2
  • Results

    With isolation rate 0.5, the outbreak could end in around 50 days, and medical-resource needs would peak at about day 35.

    Source: §5 · p. 10
  • Takeaways & Limitations

    The authors conclude that isolation is essential for controlling the spread of 2019-nCoV.

    Source: §5 · p. 10

    The model fixes spread rate β and assumes no isolation measures before T=t0+15 in the simulation.

    Source: §2 · p. 5, §3 · p. 7

Abstract

from arXiv · show

In this paper, we propose a novel dynamical system with time delay to describe the outbreak of 2019-nCoV in China. One typical feature of this epidemic is that it can spread in latent period, which is therefore described by the time delay process in the differential equations. The accumulated numbers of classified populations are employed as variables, which is consistent with the official data and facilitates the parameter identification. The numerical methods for the prediction of outbreak of 2019-nCoV and parameter identification are provided, and the numerical results show that the novel dynamic system can well predict the outbreak trend so far. Based on the numerical simulations, we suggest that the transmission of individuals should be greatly controlled with high isolation rate by the government.

1 Introduction

The paper motivates a time-delay model for an outbreak that can spread during the latent period and uses accumulated case counts as its variables. It also introduces isolation as a modeled process.

1 Introduction

  • The introduction describes early interventions as having questionable effectiveness and efficiency amid more than 11,000 confirmed cases in China.It also reports more than 3,000 confirmed cases in Wuhan and cases in multiple other countries.Source: §1 · p. 2
  • Latent-period transmission distinguishes this outbreak from SARS and makes classical SIR, SEIR, and SEIJR models inappropriate for describing it, according to the authors.The authors use the available average latent and treatment periods to motivate a time-delay process.Source: §1 · p. 2
  • The Chinese health commission reports accumulated diagnosed, cured, and dead cases, which the authors use as model variables because they are more numerically stable than instantaneous increments.The accumulated variables also align with the official data.Source: §1 · p. 2
  • The model introduces isolation to represent government measures for suspected cases and contacted individuals.The introduction identifies isolation and travel restrictions among the implemented interventions.Source: §1 · p. 3

2 A Novel Dynamical System with Time Delay

The model represents the outbreak with accumulated population variables and time-delayed processes for transmission, diagnosis, isolation, and recovery. It uses diagnosed and cured counts for parameter identification because those observations are available in official data.

2 A Novel Dynamical System with Time Delay

  • The model treats I(t) − G(t) − J(t) as the exposed population able to transmit, and β as a fixed spread rate.The authors note that β might depend on time as virus activity and the environment change.Source: §2 · p. 5
  • Diagnosed increments depend on the history of infections, with average infection-to-diagnosis delay τ1 and a normalized distribution over prior infection times.The model allows a normal distribution for that delay, or a delta function when individuals share the same latent and treatment period.Source: §2 · p. 5
  • Isolation and recovery are also modeled with delay processes, including newly isolated exposed people and cured people arising from infections at an earlier time.The recovery delay reflects the average time from infection to cure.Source: §2 · pp. 5–6
  • The model is a time-delay dynamical system whose closed-system formulation is obtained by substituting the infection increment into the delay terms.It uses accumulated infected, diagnosed, isolated, and cured populations as variables.Source: §2 · pp. 3–6
  • Parameter identification uses cumulative diagnosed J(t) and cured R(t), which are available in official data, rather than typically unobservable I(t) and G(t).R(t) does not affect the forward evolution of I(t), J(t), and G(t), but its observation may help infer parameters and initial conditions.Source: §2 · p. 6

3 The Reconstruction and Prediction Scheme

The reconstruction scheme estimates parameters from reported diagnosed and cured counts, then numerically solves the model to predict the population trajectories. Its simulations assume no isolation measures during the first 15 days after the initial time.

3 The Reconstruction and Prediction Scheme

  • The simulation assumes I(t0)=5 and G(t0)=J(t0)=R(t0)=0, with no isolation measures before T=t0+15.The initial condition represents five infections from unknown sources and no diagnosed, isolated, or recovered people on the initial day.Source: §3 · pp. 6–7
  • The scheme treats the average latent and treatment periods as known according to official data.It also sets morbidity γ to 0.99 based on present data.Source: §3 · p. 7
  • Reported diagnosed and cured counts from the National Health Commission of China are the observations used in the reconstruction scheme.The paper identifies them as JObs. and RObs.Source: §3 · p. 7
  • The scheme fits θ from official diagnosed-count data, then estimates κ from cured-count data using the recovered θ, and numerically predicts J(t), R(t), I(t), and G(t).The paper names Levenberg–Marquardt and MCMC as suitable methods for the optimization problems.Source: §3 · p. 7

4 Numerical Test

Numerical experiments test the model through isolation simulations and national and local outbreak predictions. The authors conclude that the system can predict outbreak tendency, while estimated outcomes depend on population size and local public policy.

Basic simulation

  • With isolation rate ℓ=0.6, cumulative infected people tend to about 14,000 after 40 days, while without isolation they tend to infinity.Figure 2 compares simulations with different isolation rates.Source: Figure 2 · p. 8, §4 · p. 8

Global and local outbreak

  • The 18th-day predictions are tested after parameter inference from 10 days of national data and 17 days of local city/province data.Figure 3(a) shows the national test; panels 3(b)–3(d) show local cases.Source: §4 · pp. 8–9, Figure 3 · p. 9
  • Figure 3 distinguishes observed cumulative diagnosed and cured data used for reconstruction from reconstructed values and observations used to evaluate predictions.The passage names these series JObs., RObs., JReconstr., RReconstr., JObs.2, and RObs.2.Source: §4 · p. 9, Figure 3 · p. 9

Conclusion

  • The authors conclude that the time-delay system can predict outbreak tendency and that the situation would improve.This conclusion follows their review of Figure 3 and reconstructed parameters in Table 2.Source: §4 · p. 9
  • The estimated parameters indicate that event evolution depends strongly on population size and local-government public policy.Source: §4 · p. 9

5 Concluding Remarks

The time-delay dynamical system uses infection history to represent latent-period transmission and approximates the outbreak data. The authors report isolation-related projections and identify model extensions for future work.

  • With isolation rate 0.5, the outbreak may end in around 50 days, while medical-resource needs may peak around day 35.Source: §5 · p. 10
  • The time-delay term is effective for modeling transmission during the latent period, but the current system assumes time-independent parameters.Future work may let isolation strength and spread rate vary over time to improve agreement between real data and estimated solutions.Source: §5 · p. 10
  • J(t) − R(t) represents people in treatment and may also be used in the inverse problem; external source terms may represent process uncertainty.Source: §5 · p. 10
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