Epidemiological Characteristics and Transmissibility for SARS-CoV-2 of Population Level and Cluster Level in a Chinese City

Abstract

Background: To date, there is a lack of sufficient evidence on the type of clusters in which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most likely to spread. Notably, the differences between cluster-level and population-level outbreaks in epidemiological characteristics and transmissibility remain unclear. Identifying the characteristics of these two levels, including epidemiology and transmission dynamics, allows us to develop better surveillance and control strategies following the current removal of suppression measures in China.

Methods: We described the epidemiological characteristics of SARS-CoV-2 and calculated its transmissibility by taking a Chinese city as an example. We used descriptive analysis to characterize epidemiological features for coronavirus disease 2019 (COVID-19) incidence database from 1 Jan 2020 to 2 March 2020 in Chaoyang District, Beijing City, China. The susceptible-exposed-infected-asymptomatic-recovered (SEIAR) model was fitted with the dataset, and the effective reproduction number (R_eff ) was calculated as the transmissibility of a single population. Also, the basic reproduction number (R₀) was calculated by definition for three clusters, such as household, factory and community, as the transmissibility of subgroups.

Results: The epidemic curve in Chaoyang District was divided into three stages. We included nine clusters (subgroups), which comprised of seven household-level and one factory-level and one community-level cluster, with sizes ranging from 2 to 17 cases. For the nine clusters, the median incubation period was 17.0 days [Interquartile range (IQR): 8.4-24.0 days (d)], and the average interval between date of onset (report date) and diagnosis date was 1.9 d (IQR: 1.7 to 6.4 d). At the population level, the transmissibility of the virus was high in the early stage of the epidemic (R_eff = 4.81). The transmissibility was higher in factory-level clusters (R₀ = 16) than in community-level clusters (R₀ = 3), and household-level clusters (R₀ = 1).

Conclusions: In Chaoyang District, the epidemiological features of SARS-CoV-2 showed multi-stage pattern. Many clusters were reported to occur indoors, mostly from households and factories, and few from the community. The risk of transmission varies by setting, with indoor settings being more severe than outdoor settings. Reported household clusters were the predominant type, but the population size of the different types of clusters limited transmission. The transmissibility of SARS-CoV-2 was different between a single population and its subgroups, with cluster-level transmissibility higher than population-level transmissibility.

Keywords: COVID-19; cluster-level; mathematical model; population-level; transmissibility.

Figure 1

Research technical route. The letter N represents number of symptomatic and asymptomatic infected cases in Chaoyang District, China in 2020, while n represents number of clusters reported. Symptoms onset indicates date of illness onset for symptomatic cases, while report date indicates first RT-PCR positive result for asymptomatic infections. Confirmed time indicates date of diagnosis for both infections.

Figure 2

Geographical distribution of SARS-CoV-2 symptomatic and asymptomatic infected cases in Chaoyang District, China (2020). (A) Beijing City; (B) Chaoyang District; The map depicted in this figure was taken from Wikimedia Commons (http://commons.wikimedia.org/wiki/Main_Page).

Figure 3

SEIAR model for simulating COVID-19.

Figure 4

Daily number of SARS-CoV-2 infections stratified by source of infection in Chaoyang District, China (2020).

Figure 5

Distributions for type of cluster and presence of symptoms of nine COVID-19 clusters reported from Chaoyang District, China (2020). Type of cluster depends on the setting where exposure took place, with primary cases considered as first generation. Presence of symptoms include symptomatic and asymptomatic infections.

Figure 6

Fitting results of the SEIAR model and the data of the actual secondary cases of SARS-CoV-2 infections.

Figure 7

Timing of transmission events in seven household-level clusters. Square symbols indicate symptomatic infections and circular symbols indicate asymptomatic infections. Blue grids indicate primary case and purple grids indicate secondary cases. Age, sex, and generation in a cluster are shown for each SARS-CoV-2 infected individuals, with information of date of illness onset (symptoms onset) for symptomatic cases and date of the first RT-PCR positive result (report date) for asymptomatic infections and date of diagnosis (confirmed time) for both infections. Timeline of transmission also includes the first and last contact time between the primary case and secondary cases. Except for community-level cluster where there is no contact time due to contacts via public objects, all other types of clusters have first contact time and last contact time between secondary cases and primary cases. The illustrations of Figure 7 and Figure 8 are the same as here.

Figure 8

Timing of transmission event in one factory-level cluster.

Figure 9

Timing of transmission event in one community-level cluster.