Revised SEIR model
COVID-19 is a disease caused by the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Langousis and Carsteanu 2020; Sivakumar 2020) which is genetically related to the coronavirus responsible for the SARS outbreak of 2003 (World Health Organization 2020b). To model the epidemiological progression of COVID-19, the transmission model for SARS (Lipsitch et al. 2003) was adapted. The transmission model for SARS is a modification of the standard SEIR model (Anderson and May 1991). The standard SEIR model tracks susceptible, exposed (infected but not yet infectious), infectious and recovered individuals in the compartments S, E, I and R, respectively, whereas the Lipsitch transmission model further incorporates quarantine measures into the SEIR model. Specifically, susceptible individuals are divided into ‘susceptible’ and ‘susceptible but isolated’ (compartments \( S \) and \( S_{Q} \)), exposed individuals are divided into ‘exposed’ and ‘exposed but isolated’ (compartments \( E \) and \( E_{Q} \)) and infectious individuals are divided into ‘those who have not been isolated’ (\( I_{U} \)), and ‘those who have been hospitalized’ (\( I_{D} \)). Based on the evidence for indirect transmission resulting from transmission by asymptomatic infected persons and pre-symptomatic transmission (Cai et al. 2020; Tong et al. 2020; Bai et al. 2020; Nishiura et al. 2020; Rothe et al. 2020), we further modified the model by assuming that a fraction \( p \) of all infectious persons are asymptomatic (\( 1 - p \) of all infectious persons are symptomatic), that a proportion \( b_{a} \) of people who make contact with an asymptomatic person are infected, and a proportion \( b_{s} \) of people who make contact with a symptomatic person are infected. In this situation, the probability of a susceptible person becoming infected by contacting an infectious person is \( b_{s} \left( {1 - p} \right) + b_{a} p \), and the probability of a susceptible who makes contact not becoming infected is \( \left( {1 - b_{s} } \right)\left( {1 - p} \right) + \left( {1 - b_{a} } \right)p \). For simplicity, we use the notation \( b \) to represent \( b_{s} \left( {1 - p} \right) + b_{a} p \) and \( 1 - b \) to represent \( \left( {1 - b_{s} } \right)\left( {1 - p} \right) + \left( {1 - b_{a} } \right)p \). In addition, we model the situation in which Beijing faces the return of considerable numbers of people from elsewhere in the country; thus, two parameters \( {\text{S}}_{B}^{t} \) and \( {\text{E}}_{B}^{t} \) are incorporated into the model, representing imported susceptible people and imported exposed people, respectively. That is,
$$ \begin{aligned} & {\text{d}}S/{\text{d}}t = S_{B}^{t} - \left( {b + \left( {1 - b} \right)q} \right)k_{t} I_{U} S/N0 + r_{Q} S_{Q} \\ & {\text{d}}S_{Q} /{\text{d}}t = \left( {1 - b} \right)k_{t} I_{U} qS/N0 - r_{Q} S_{Q} \\ & {\text{d}}E/{\text{d}}t = \left( {1 - q} \right)E_{B}^{t} + b\left( {1 - q} \right)k_{t} I_{U} S/N0 - rE \\ & {\text{d}}E_{Q} /{\text{d}}t = qE_{B}^{t} + bqk_{t} I_{U} S/N0 - rE_{Q} \\ & {\text{d}}I_{U} /{\text{d}}t = rE - \left( {v + m + w} \right)I_{U} \\ & {\text{d}}I_{D} /{\text{d}}t = rE_{Q} + wI_{U} - \left( {v + m} \right)I_{D} \\ & {\text{d}}R/{\text{d}}t = v\left( {I_{U} + I_{D} } \right) \\ & {\text{d}}\left( {dead} \right)/{\text{d}}t = m\left( {I_{U} + I_{D} } \right) \\ \end{aligned} $$
(1)
It should be noted that the superscript \( t \) in \( {\text{S}}_{B}^{t} \) and \( {\text{E}}_{B}^{t} \) indicates the stage of resuming work. For different stages of resuming work, there will be different populations of imported migrants. In this study, the resumption rate is reflected by the corresponding proportion of imported migrants. Moreover, during the specific stage of resuming work, the daily contact number per capita is determined by the corresponding reopened socio-economic factors, denoted by \( k_{t} \). That is the parameter \( k_{t} \) in the revised SEIR model varies with the resumption rate, because reopened businesses at different stages of resumption have different abilities to attract people. At the initial stage of resuming work, there were only essential services reopened. To reflect the ability of these reopened essential services attracting people, we used the density of POI regarding the essential services to characterize the value of the parameter \( k_{t} \) for this initial stage. The mean daily rate at which infectious cases are detected and isolated is determined by the medical capacity which is denoted by \( w \). This parameter \( w \) is constant because medical resources were at full operation in the initial stages of resumption. The other parameters in Eq. (1) are independent of resumption rate, and are also considered constant in this study. Figure 1 illustrate the mechanism for our transmission model.
The classic SEIR model is accepted widely as a basic model to describe the properties of COVID-19 transmission. Hou et al. (2020) and He et al. (2020a) employed a mixed SEIR compartmental model assuming that susceptible individuals contacting an exposed individual would probably become infected. Yang et al. (2020) modified the original SEIR model, introducing move-in and move-out parameters, because the initial outbreak of COVID-19 in China occurred during the Spring Festival. At that time, hundreds of millions of people moved between the provinces of China. Despite these modifications some properties of COVID-19 transmission, particularly pandemic-prevention measures, were not considered. Therefore, here, a quarantined component is added into the classic SEIR model as a fifth element in addition to the four elements: S (susceptible), E (exposed), I (infectious) and R (recovered) (Lopez and Rodó 2020). Furthermore, He et al. (2002b) added another element, hospitalized, representing the part of the infectious population that cannot contact other people. Infectious individuals still active in society and potentially spreading the virus should be distinguished from hospitalized infectious individuals. Wei et al. (2020) considered a more detailed scenario, where asymptomatic infected persons are introduced. In contrast, our model incorporates the above considerations into the classic SEIR model with some simplifications providing a comprehensive characterization of the properties of COVID-19 transmission in Beijing.
Estimating the reproductive number
In the absence of quarantine, the reproductive number for this model is given by \( R = bkD \), where \( D \) is the mean duration of infectiousness, \( D = 1/\left( {v + m + w} \right) \). The effect of quarantining a fraction q of contacts of infectious persons is to multiply this expression by \( \left( {1 - q} \right) \) (Lipsitch et al. 2003). On the other hand, the reproductive number can be calculated deterministically by the formula \( R = 1 + v\lambda + f\left( {1 - f} \right)\left( {v\lambda } \right)^{2} \), where \( f \) is the ratio of the infectious period to the serial interval. \( v \) is the sum of the mean infectious and mean latent periods, and \( \lambda \) is the exponential growth rate of the cumulative number of cases in the pandemic (Lipsitch et al. 2003).
Data collection and preprocessing
Pandemic data for Beijing were collected from the website of the Beijing Municipal Health Commission (http://wjw.beijing.gov.cn/xwzx_20031/wnxw/) including daily confirmed cases, daily recovered cases and daily death cases for Beijing Municipality, as well as the total confirmed cases for each district of Beijing Municipality. The Beijing pandemic was first reported on 20 January 2020. To initialize the model, we assume that there were only exposed individuals at that time as a result of passenger inflow from Wuhan direct to Beijing. After the travel ban from Wuhan, the growth of the pandemic in Beijing can be viewed as based on internal progression within Beijing without further imported cases (Tian et al. 2020).
With Beijing reopened, socio-economic factors and medical capacity within the different districts of Beijing play important roles in the evolution of the epidemic. To better describe the evolution of the epidemic in Beijing, we collected multi-source data with which to fit the revised SEIR model. Socio-economic factors and medical capacity are described by the densities (pcs per square kilometer) of socio-economic activity places (SEAPs) and medical services, respectively, within each district of Beijing. The density of SEAPs for each district is measured by the density of POIs (points of interest) collected from the Gaode Map API (https://lbs.amap.com/api/webservice/guide/api/search) including 10 major categories: Accommodation Services, Governmental Organization, Financial and Insurance Services, Commercial Business, Enterprises, Shopping, Food and Beverages, Transportation Services, Science/Culture and Education Services, and Sports and Recreation. Medical Services per se is a major category of the POI data. Thus, the corresponding densities were used directly to describe the medical capacity for each district.
With respect to SEAPs, each major category consists of related granular categories, each of which has different population flows. Therefore, we assigned weights to the granular categories to calculate the density of each major category, specifically as the weighted average of the densities of the corresponding granular categories (see Table 5 in “Appendix”). For example, the major category Accommodation Services includes two granular categories, Hotel and Hostel. Because Hotel had a smaller population flow than Hostel, the weights of Hotel and Hostel were set as 0.4 and 0.6, respectively. It should be noted that the weights here represent the relative, rather than the absolute, magnitude. The densities of the other nine major categories were obtained in the same way. Next, the density of SEAPs was obtained by the weighted average of the densities of the 10 major categories, wherein the weights of the major categories were pre-defined according to their relative population flows also (see Table 5 in “Appendix”). Medical capacity was quantified by the density of medical services consisting of four granular categories in a similar way, but with the weights for the four granular categories of medical services pre-defined based on their theme relevance to the epidemic (see Table 5 in “Appendix”). For example, the largest weight was assigned to the granular category, Special Hospital, because one of the themes of it is infectious disease. The POI dataset was generated in 2017, while the acquisition time was March 2020. Population numbers of both residents and in-migrants for each district of Beijing were collected from the Beijing Statistical Yearbook in 2019 (Beijing Municipal Bureau Statistics 2019).
We employed non-linear least squares for parameter estimation by minimizing the distance between the predicted \( I_{D} \), \( R \), dead and corresponding observed numbers from 20 January 2020 to 20 March 2020. With respect to the parameters, the duration of quarantine, the average time of progression from latent infection to infectious, the proportion of asymptomatic cases and the per capita death rate were determined according to relevant reports (World Health Organization 2020c; Lauer et al. 2020; Mizumoto et al. 2020; Xia et al. 2020). The imported exposed population, the daily number of contacts per capita, the fraction of all persons contacted by an infectious person who are successfully quarantined, the per capita recovery rate, the transmission probability and the mean daily rate at which infectious cases are detected and isolated are estimated and given in Table 1. For each district of Beijing, we assumed that all parameters were the same as for the greater Beijing Municipality, except the daily contact number \( k \), detection rate \( w \) and quarantine fraction \( q \). The first two parameters are considered to reflect the spatial heterogeneity of people’s behavior and the medical capacity of each district. Districts with more companies and schools, for example, tend to have larger daily contact numbers. To reduce the uncertainty of the model, we employed socio-economic factors and medical capacity in the evaluation of the parameters \( k \) and \( w \), respectively. The socio-economic factors and medical capacity were determined by the POI data. That is the parameters \( k \) and \( w \) were determined by the densities of SEAPs and medical services regarding the whole Beijing Municipality. Then, the quarantine fraction \( q \) of each district was estimated based on local pandemic data with a fixed daily contact number \( k \) and detection rate \( w \). Under the circumstances, we set the local resident population as the susceptible population for each district.
Table 1 Initial conditions and parameters for the Beijing pandemic For simplicity, the districts of Beijing Municipality are named as follows: DC (Dongcheng District); XC (Xicheng District); CY (Chaoyang District); FT (Fengtai District); SJS (Shijingshan District); HD (Haidian District); MTG (Mentougou District); FS (Fangshan District); TZ (Tongzhou District); SY (Shunyi District); CP (Changping District); DX (Daxing District); HR (Huairou District); PG (Pinggu District); MY (Miyun District); YQ (Yanqing District).