Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan

Abstract

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

Figure 1

Number of clusters reported by epidemiological week, cluster type, and cluster size (the number of persons infected, indicated by circle size). “Cluster” is defined as with at least five confirmed cases within a common event or venue.

Figure 2

(A) Epidemic curve (based on confirmed date) with colored boxes indicating dominant variants at each time period, (B) Effective reproduction number ($R_t$, or R on the chart), red line was estimated from the daily number of cases, (C) time-varying dispersion parameter ($k_t$, k on the chart), (D) the proportion of cases infecting 80% ($P_{80}$, Prop_80 on the chart), and (E) the proportion of cases who did not spread to anyone ($P_0$, Prop_0 on the chart) for each generation of transmission in Yamagata, Japan between 2020 November 1 and 2022 January 19. In Panel (A), (1) ~ (5) indicates each wave. In Panel (B–E), the shaded areas show the 95% CrI. SOE: State of emergency, G1: first-generation, G2+: second-generation or later, All: All generation.

Figure 3

The observed offspring distribution of the number of secondary cases from G1 and G2+ cases in Yamagata, Japan. G1: first-generation, G2+: second-generation or later.