Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak

Abstract

Background: Various models have been applied to predict the trend of the epidemic since the outbreak of COVID-19.

Methods: In this study, we designed a dynamic graph model, not for precisely predicting the number of infected cases, but for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors.

Results: We demonstrated the impact of asymptomatic transmission in this outbreak and showed the effectiveness of city lockdown to halt virus spread within a city. We further illustrated that sudden emergence of a large number of cases could overwhelm the city medical system, and external medical aids are critical to not only containing the further spread of the virus but also reducing fatality.

Conclusion: Our model simulation showed that highly populated modern cities are particularly vulnerable and lessons learned in China could facilitate other countries to plan the proactive and decisive actions. We shall pay close attention to the asymptomatic transmission being suggested by rapidly accumulating evidence as dramatic changes in quarantine protocol are required to contain SARS-CoV-2 from spreading globally.

Graphical abstract

Keywords

dynamic graph model / transportation / COVID-19 / SARS-CoV-2

References

[1] Coronavirus disease. 2019(COVID-19) Situation Report – 29. Available at https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200219-sitrep-30-covid-19.pdf?sfvrsn=6e50645_2 (Accessed: Mar 25, 2020)

[2] Read, J. M., Bridgen, J. R., Cummings, D. A., Ho, A. and Jewell, C. P. (2020) Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions. medRxiv, 20018549

[3] Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., (2020) Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N. Engl. J. Med., 382, 1199–1207

[4] Tian, H., Liu, Y., Li, Y., Kraemer, M. U. G., Chen, B., Wu, C.-H., Cai, J., Li, B., Xu, B., Yang, Q., (2020) Early evaluation of transmission control measures in response to the 2019 novel coronavirus outbreak in China. medRxiv, 20019844

[5] Anastassopoulou, C., Russo, L., Tsakris, A. and Siettos, C. (2020) Data-based analysis, modelling and forecasting of the novel coronavirus (2019-nCoV) outbreak. PLoS ONE 15, e0230405

[6] Gilbert, M., Pullano, G., Pinotti, F., Valdano, E., Poletto, C., Boëlle, P.-Y., D’Ortenzio, E., Yazdanpanah, Y., Eholie, S.P., Pharm, M.A., (2020) Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study. The Lancet. 395, 871–877

[7] Wang, D., Hu, B., Hu, C., Zhu, F., Liu, X., Zhang, J., Wang, B., Xiang, H., Cheng, Z., Xiong, Y., (2020) Clinical Characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA, 323,1061–1069

[8] Casella, F. (2020) Can the COVID-19 epidemic be managed on the basis of daily data? arXiv, 2003.06967

[9] Tang, Z., Li, X., and Li, H. (2020) Prediction of new coronavirus infection based on a modified SEIR model. medRxiv, 20030858

[10] Guo, D. (2007) Visual analytics of spatial interaction patterns for pandemic decision support. Int. J. Geogr. Inf. Sci., 21, 859–877

[11] Chang, D., Lin, M., Wei, L., Xie, L., Zhu, G., Dela Cruz, C. S., and Sharma, L. (2020) Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China. JAMA, 323, 1092–1093

[12] Zou, L., Ruan, F., Huang, M., Liang, L., Huang, H., Hong, Z., Yu, J., Kang, M., Song, Y., Xia, J., (2020) SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N. Engl. J. Med., 382, 1177–1179

[13] Chan, J. F.-W., Yuan, S., Kok, K.-H., To, K. K., Chu, H., Yang, J., Xing, F., Liu, J., Yip, C. C., Poon, R. W., (2020) A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet, 395, 514–523

[14] Wenzel, P., Kopp, S., Göbel, S., Jansen, T., Geyer, M., Hahn, F., Kreitner, K., Escher, F., Schultheiss, H.P., and Münzel, T. (2020) Evidence of SARS-CoV-2 mRNA in endomyocardial biopsies of patients with clinically suspected myocarditis tested negative for COVID-19 in nasopharyngeal swab. Cardiovasc. Res., 116, 1661–1663

[15] Epidemiology Working Group for NCIP Epidemic Response, Chinese Center for Disease Control and Prevention. (2020) The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China. Chinese Journal of Epidemiology, 41, 145–151, in Chinese

[16] Guan, W. J., Ni, Z. Y., Hu, Y., Liang, W. H., Ou, C. Q., He, J. X., Liu, L., Shan, H., Lei, C. L., Hui, D. S. C., , (2020) Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med., 382, 1708–1720

SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.1007/s40484-020-0215-4.

CODE AVAILABILITY

https://github.com/xjtu-omics/2019-nCoV_graph_model.

AUTHOR CONTRIBUTIONS

K.Y. conceived of and designed the study. X.Y. and T.X. implemented the code. X.Y. and P.J. collected and analyzed the data. K.Y., X.Y., H.X., L.Z., L.G. interpreted the results. X.Y. produced the figures. K.Y., X.Y. and L.G. drafted the Article. All authors contributed to the writing of the final version of the Article.

ACKNOWLEDGEMENTS

This study was supported by the National Key R&D Program of China (Nos. 2018YFC0910400, 2017YFC0907500, and 2018ZX10302205), the National Natural Science Foundation of China (Nos. 61702406, 3161372, 31701739 and 8191101420), the “World-Class Universities and the Characteristic Development Guidance Funds for the Central Universities”, Xi’an Jiaotong University Basic Research and Profession Grant (No. xtr022019003), and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Xiaofei Yang, Tun Xu, Peng Jia, Han Xia, Li Guo, Lei Zhang and Kai Ye declare that they have no conflict of interests.

All procedures performed in studies were in accordance with the ethical standards of the institution or practice at which the studies were conducted, and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

RIGHTS & PERMISSIONS

2020 Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature