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Analysis on early spatiotemporal transmission characteristics of COVID-19

Wang Cong Yan Jie Wang Xu Li Min

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Analysis on early spatiotemporal transmission characteristics of COVID-19

Wang Cong, Yan Jie, Wang Xu, Li Min
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  • In this paper, a simple susceptible-infected (SI) model is build for simulating the early phase of COVID-19 transmission process. By using the data collected from the newest epidemiological investigation, the parameters of SI model is estimated and compared with those from some other studies. The population migration data during Spring festival in China are collected from Baidu.com and also extracted from different news sources, the migration characteristic of Wuhan city in the early phase of the epidemic situation is captured, and substituted into a simple difference equation model which is modified from the SI model for supporting migrations. Then several simulations are performed for the spatiotemporal transmission process of COVID-19 in China. Some conclusions are drawn from simulations and experiments below. 1) With 95% confidence, the infection rate of COVID-19 is estimated to be in a range of 0.2068–0.2073 in general situation, and the corresponding basic reproduction number R0 is estimated to be in a range of 2.5510–2.6555. A case study shows that under an extreme condition, the infection rate and R0 are estimated to be 0.2862 and 3.1465, respectively. 2) The Pearson correlation coefficient between Baidu migration index and the number of travelers sent by railway is 0.9108, which indicates a strong linear correlation between them, thus it can be deduced that Baidu migration index is an efficient tool for estimating the migration situation. 3) The epidemic arrival times for different provinces in China are estimated via simulations, specifically, no more than 1 day within an estimation error of 41.38%; no more than 3 days within an error of 79.31%, and no more than 5 days with an error of 95.55%. An average estimation error is 2.14 days.
      Corresponding author: Yan Jie, yan_jie@foxmail.com
    • Funds: Project supported by the National Natural Science Foundation of China (Grant No. 61602331)
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    Li Q, Guan X H, Wu P, Wang X Y, Zhou L, Tong Y Q, Ren R Q, Leung S, Lau E, Wong J, Xing X S, Xiang N J, Wu Y, Li C, Chen Q, Li D, Liu T, Zhao J, Li M, Tu W X, Chen C D, Jin L M, Yang R, Wang Q, Zhou S H, Wang R, Liu H, Luo Y B, Liu Y, Shao G, Li H, Tao Z F, Yang Y, Deng Z Q, Liu B X, Ma Z T, Zhang Y P, Shi G Q, Lam T, Wu J, Gao G, Cowling B, Yang B, Leung G, Feng Z J 2020 N. Engl. J. Med. 382 1199Google Scholar

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    Cao S L, Feng P H, Shi P P 2020 J. Zhejiang Univ. 49 1Google Scholar

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    范如国, 王奕博, 罗明, 张应青, 朱超平 2020 电子科技大学学报 (in press)Google Scholar

    Fan R G, Wang Y B, Luo M, Zhang Y Q, Zhu C P 2020 J. Univ. Electron. Sci. & Tech. China (in pressGoogle Scholar

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    Dirk B, Helbing D 2013 Science 342 1337Google Scholar

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    Wu J T, Leung K, Leung G M 2020 Lancet 395 e41Google Scholar

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    Wang J, Wang X, Wu J 2018 Proceedings of the 24th ACM SIGKDD Conference on Knowledge Discovery and Data Mining London, United Kingdom, Augest 19–23, 2018 p2830

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    Yang Z F, Zeng Z Q, Wang K, Wong S S, Liang W H, Zanin M, Liu P, Cao X D, Gao Z Q, Mai Z T, Liang J Y, Liu X Q, Li S Y, Li Y M, Ye F, Guan W J, Yang Y F, Li F, Luo S M, Xie Y Q, Liu B, Wang Z L, Zhang S B, Wang Y N, Zhong N S, He J X 2020 J. Thorac. Dis. 12 2077

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    Baidu.com. https://qianxi.baidu.com [2020-3-10]

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    Chinese Center for Disease Control and Prevention. http://www.chinacdc.cn[2020-3-10]

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    Cohen J 2020 https://www.sciencemag.org/news/2020/02/scientists-are-racing-model-next-moves-coronavirus-thats-still-hard-predict[2020-3-10]

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    中国疾病预防控制中心新型冠状病毒肺炎应急响应机制流行病学组 2020 中华流行病学杂志 41 145Google Scholar

    The Novel Coronavirus Pneumonia Emergency Response Epidemiology Team 2020 Chin. J. Epidemiol. 41 145Google Scholar

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    Chen X L, Zhou T S, Feng L, Liang J B, Lilgeros F, Havlin S, Hu Y Q 2019 Phys. Rev. E 100 032310

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    Wang J, Wang L, Li X 2016 IEEE Trans. Cybernetics 46 2782Google Scholar

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    Chen L M, Holzer M, Shapiro A 2018 Chaos 28 013105Google Scholar

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    Chowell G, Viboud C, Hyman J, Simonsen L 2015 PLoS Currents 7 1

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    Viboud C, Simonsen L, Chowell G 2016 Epidemics-Neth 15 27Google Scholar

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    Chen D B, Zhou T 2008 arXiv: 2003.00305 v1[Quantitative Biology]

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    Wallinga J, Lipsitch M 2007 Proc. R. Soc. Lond, B 274 599Google Scholar

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    Guan W J, Ni Z Y, Hu Y, Liang W H, Ou C Q, He J X, Liu L, Shan S, Lei C L, Hui D, Du B, Li L J, Zeng G, Yuen K, Chen R C, Tang C L, Wang T, Chen P Y, Xiang J, Li S Y, Wang J L, Liang Z J, Peng Y X, Wei L, Liu L, Hu Y H, Peng P, Wang J M, Liu J Y, Chen Z, Li G, Zheng Z J, Qiu S Q, Luo J, Ye C J, Zhu S Y, Zhong N N 2020 N. Engl. J. Med. (in press)Google Scholar

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    Lipsitch M, Cohen T, Cooper B, Robins J, Ma S, James L, Gopalakrishna G, Chew S K, Tan C C, Samore M, Fisman D, Murray M 2003 Science 300 1966Google Scholar

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    Ho H, Fraser C, Lam T, Ghani C, Leung G, Leung G, Chau Y K, Ho P L, Lo , Abu-Raddad L, Donnelly C, Anderson D, Chan K, Lee K, Lau E, Hedley A, RileyS, Tsang T, Ferguson N, Thach D T 2003 Science 300 1961Google Scholar

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    Wallinga J, Teunis P 2004 Am. J. Epidemiol. 160 509Google Scholar

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  • 图 1  不同的$\beta $取值下实际累积发病人数与预测发病人数的对比 (a) 2019年; (b) 2020年

    Figure 1.  Comparing the actual cumulative number of cases and its estimations according to different$\beta $: (a) Year 2019; (b) year 2020.

    图 2  武汉“封城”前夕迁徙指数与2019年的对比 (a)迁入规模指数; (b) 迁出规模指数

    Figure 2.  Comparing the migration index of Wuhan before the spring festival with the same period of 2019: (a) Inner migration index; (b) outer migration index.

    图 3  各省区首达病例时间预测误差

    Figure 3.  The estimation errors of the first arrival times for each provinces.

    表 1  2019年累积发病人数

    Table 1.  The cumulative number of confirmed cases in 2019.

    日期人数日期人数日期人数日期人数日期人数
    12/09112/171212/212912/254712/2978
    12/11212/181412/223712/264912/3090
    12/12512/191612/234012/275912/31102
    12/15812/202512/244512/2868
    DownLoad: CSV

    表 2  2020年各时间段累积发病人数

    Table 2.  The cumulative number of confirmed cases in each time slots in 2020.

    截至时点估计发病人数实际发病人数上报CCDC人数
    软件抓取法蒙特卡罗法
    2019/12/31102491020
    2020/01/10738459738—78141
    2020/01/20616258006143—6187291
    2020/01/31326612965432633—3267711821
    2020/02/1144692691634467244730
    DownLoad: CSV

    表 3  传染率$\beta $可能的取值

    Table 3.  Possible values of the infection rate.

    截止日期$\beta $置信区间R2截止日期$\beta $置信区间R2
    2019/12/310.2213[0.2152, 0.2274]0.8682020/01/110.2066[0.2056, 0.2274]0.990
    2020/01/010.2171[0.2116, 0.2225]0.8782020/01/120.2063[0.2056, 0.2071]0.993
    2020/01/020.2168[0.2127, 0.2209]0.92320200/1/130.2060[0.2054, 0.2067]0.995
    2020/01/030.2159[0.2127, 0.2191]0.9492020/01/140.2059[0.2054, 0.2064]0.997
    2020/01/040.2155[0.2130, 0.2179]0.9672020/01/150.2056[0.2052, 0.2060]0.998
    2020/01/050.2138[0.2118, 0.2159]0.9732020/10/160.2058[0.2054, 0.2061]0.998
    2020/01/060.2127[0.2109, 0.2144]0.9802020/01/170.2060[0.2057, 0.2063]0.999
    2020/01/070.2109[0.2093, 0.2126]0.9802020/01/180.2064[0.2061, 0.2066]0.999
    2020/01/080.2091[0.2075, 0.2107]0.9792020/01/190.2065[0.2063, 0.2067]0.999
    2020/01/090.2080[0.2067, 0.2094]0.9842020/01/200.2066[0.2064, 0.2068]0.999
    2020/01/100.2067[0.2054, 0.2080]0.9852020/01/210.2070[0.2068, 0.2073]0.999
    DownLoad: CSV

    表 4  重要时间节点的累积发病人数

    Table 4.  Cumulative confirmed cases in key time nodes.

    截至时点$\beta $
    0.22130.21590.20800.2066
    2019/12/311301169795
    2020/01/1011901001777753
    2020/01/2010870866662205964
    DownLoad: CSV

    表 5  武汉市三大火车站发送旅客人数与迁出指数

    Table 5.  The Baidu inner migration index and the number of the travelers sent from Wuhan`s major railway stations.

    日期迁徙指数人数/万日期迁徙指数人数/万日期迁徙指数人数/万
    2020/01/106.6232272020/01/2211.840329.962019/01/297.028227.2
    2020/01/117.561229.82019/01/214.571821.62019/01/307.107227.7
    2020/01/126.2165272019/01/224.689221.42019/01/317.480028.1
    2020/01/135.762024.82019/01/234.8062232019/02/018.714029.8
    2020/01/155.908726.52019/01/244.860521.72019/02/029.604331.5
    2020/01/166.002827.72019/01/267.0436272019/02/039.224729.1
    2020/01/197.4060302019/01/286.770626.8
    DownLoad: CSV

    表 6  省级区域的首例到达时间

    Table 6.  The arrival times of each provinces.

    省份$\beta $实际日期省份$\beta $实际日期
    0.22130.21590.20700.22130.21590.2070
    安徽01/0601/0601/0701/07辽宁01/1101/1201/1301/09
    北京01/0701/0701/0801/08*内蒙古01/1301/1401/1601/16
    福建01/0901/0901/1001/06宁夏01/1701/1801/2001/17
    甘肃01/1001/1101/1201/04青海01/1901/2101/2301/21
    广东01/0501/0501/0601/04山东01/0801/0801/0901/08
    广西01/0801/0901/0901/13山西01/0901/1001/1001/14
    贵州01/0801/0801/0901/06陕西01/0901/0901/1001/12
    海南01/1001/1101/1201/13上海01/0801/0801/0901/10
    河北01/0801/0901/0901/13四川01/0801/0801/0901/07
    河南01/0401/0401/0501/03天津01/1401/1501/1601/11
    黑龙江01/1201/1301/1401/12西藏 > 01/23 > 01/23 > 01/2301/30
    湖南01/0501/0501/0601/05新疆01/1201/1201/1401/17
    吉林01/1501/1501/1701/14云南01/0901/1101/1001/07
    江苏01/0601/0701/0701/10浙江01/0701/0701/0801/04
    江西01/0601/0701/0701/07重庆01/0801/0801/0901/06
    DownLoad: CSV
    Baidu
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    [2]

    Zhou T, Liu Q H, Yang Z M, Liao J Y, Yang K X, Bai W, Lv X, Zhang W 2020 J. Evid.-based Med. 20 3

    [3]

    Zhang S, Diao M Y, Yu W B, Pei L, Lin Z F, Chen D C 2020 Int. J. Infect. Dis. 93 201Google Scholar

    [4]

    曹盛力, 冯沛华, 时朋朋 2020 浙江大学学报 49 1Google Scholar

    Cao S L, Feng P H, Shi P P 2020 J. Zhejiang Univ. 49 1Google Scholar

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    范如国, 王奕博, 罗明, 张应青, 朱超平 2020 电子科技大学学报 (in press)Google Scholar

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    Dirk B, Helbing D 2013 Science 342 1337Google Scholar

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    Wu J T, Leung K, Leung G M 2020 Lancet 395 e41Google Scholar

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    Wang J, Wang X, Wu J 2018 Proceedings of the 24th ACM SIGKDD Conference on Knowledge Discovery and Data Mining London, United Kingdom, Augest 19–23, 2018 p2830

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    Yang Z F, Zeng Z Q, Wang K, Wong S S, Liang W H, Zanin M, Liu P, Cao X D, Gao Z Q, Mai Z T, Liang J Y, Liu X Q, Li S Y, Li Y M, Ye F, Guan W J, Yang Y F, Li F, Luo S M, Xie Y Q, Liu B, Wang Z L, Zhang S B, Wang Y N, Zhong N S, He J X 2020 J. Thorac. Dis. 12 2077

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    中国疾病预防控制中心新型冠状病毒肺炎应急响应机制流行病学组 2020 中华流行病学杂志 41 145Google Scholar

    The Novel Coronavirus Pneumonia Emergency Response Epidemiology Team 2020 Chin. J. Epidemiol. 41 145Google Scholar

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    Chen X L, Zhou T S, Feng L, Liang J B, Lilgeros F, Havlin S, Hu Y Q 2019 Phys. Rev. E 100 032310

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    Wang J, Wang L, Li X 2016 IEEE Trans. Cybernetics 46 2782Google Scholar

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    Viboud C, Simonsen L, Chowell G 2016 Epidemics-Neth 15 27Google Scholar

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    Chen D B, Zhou T 2008 arXiv: 2003.00305 v1[Quantitative Biology]

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    Ho H, Fraser C, Lam T, Ghani C, Leung G, Leung G, Chau Y K, Ho P L, Lo , Abu-Raddad L, Donnelly C, Anderson D, Chan K, Lee K, Lau E, Hedley A, RileyS, Tsang T, Ferguson N, Thach D T 2003 Science 300 1961Google Scholar

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    [20] WANG BING-HONG, WANG LEI, HUI PAK-MING, HU BAMBI. THE GRADUAL ACCELERATING TRAFFIC FLOW GELLULAR AUTOMATON MODEL IN WHICH ONLY HIG H SPEED CAR CAN BE DELAYED. Acta Physica Sinica, 2000, 49(10): 1926-1932. doi: 10.7498/aps.49.1926
Metrics
  • Abstract views:  14142
  • PDF Downloads:  175
  • Cited By: 0
Publishing process
  • Received Date:  25 February 2020
  • Accepted Date:  11 March 2020
  • Published Online:  20 April 2020

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