Wednesday, February 12, 2020

Covid-19 Spread Modeling


medrxiv |  In December 2019, Wuhan, China reported an outbreak of atypicalpneumonia caused by the 2019 novel coronavirus (2019-nCoV). As of February7, 2020, the total numberof the confirmed cases in mainland Chinareached to 34,546of whom 722have died and 2,050recovered. While most Chinese cities have confirmed cases, the city-level epidemical dynamics is unknown. The aim of this study is to model the dynamics of 2019-nCoVat city level and predict the trend under different scenarios in mainland China. Weused mobile phone data and modified the classic epidemiological Susceptible -Infectious -Recovered (SIR) model toconsider several unique characteristics of the outbreak of 2019-nCoVin mainland China. The modified SIR model was trained using the confirmed cases from January25 to February1 and validated by the data collected on February2, 2020. The predictionaccuracy of new infected cases on February 2 (R2= 0.94, RMSE = 18.24) is higher than using the classic SIR model (R2= 0.69, RMSE = 40.18). We usedthe trained model to predict the trend in the next 30 days (up to March 2, 2020) under different scenarios: keeping the early-stage trend, controlling the disease as successfully as SARS in 2003, and increasing person-to-person contactsdue to work/school resuming. Results show that the total infected population in mainland China will be 10.53, 0.15, and 0.41 million and 67%, 100%, 91% Chinese cities will control the virus spreadingby March 2, 2020 under the above three scenarios.Our study also providesthe city-level spatial pattern of the epidemic trend for decision makers to allocate resources for controllingvirusspreading. 

Wuhan, a large city with 14 million residents and a major air and train transportation hub of central China, identified a cluster of unexplained cases of pneumonia on December 29, 2019 (Li et al., 2020). Four patients were initially reported and all these initial cases were linked to the Huanan Seafood Wholesale Market (Zhu et al., 2020). Chinese health authorities and scientists did immediate investigation and isolated a novel coronavirus from these patients by January 7, 2020, which is then named as 2019-nCoVby the World Health Organization (Chen et al., 2020; Wang et al., 2020). 2019-nCoVcan cause acute respiratory diseases that progress to severe pneumonia (Huang et al., 2020). The infection fatality risk is around 3% estimated from the data of early outbreak (Perlman, 2020; Wang et al., 2020). Information on new cases strongly indicates human-to-human spread (Fuk-Woo Chan et al., 2020; Li et al., 2020; Riou and Althaus, 2020). Infection of 2019-nCoVquickly spread to other cities in China and other countries(Figure 1). It becomes an event of global health concern (Hui et al., 2020). Up to February7,2020, according to the reports published by the Chinese Center for Disease Control and Prevention, allprovinces of mainland China have confirmed cases and the total number reaches to 3,4546, of whom 722have died and 2050recovered; 24oversea countries have 285confirmed cases (1 died).Chinese government took immediate actions to control the spread of disease, including closing the public transportation from and to Wuhan on January23, extending the Spring Festival holiday, postponing the school-back day, and suspending all domestic and international group tours.