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Estimating the differences in the incubation-period, serial-interval, and generation-interval distributions of SARS-CoV-2 variants is critical to understanding their transmission. However, the impact of epidemic dynamics is often neglected in estimating the timing of infection—for example, when an epidemic is growing exponentially, a cohort of infected individuals who developed symptoms at the same time are more likely to have been infected recently. Here, we reanalyze incubation-period and serial-interval data describing transmissions of the Delta and Omicron variants from the Netherlands at the end of December 2021. Previous analysis of the same dataset reported shorter mean observed incubation period (3.2 d vs. 4.4 d) and serial interval (3.5 d vs. 4.1 d) for the Omicron variant, but the number of infections caused by the Delta variant decreased during this period as the number of Omicron infections increased. When we account for growth-rate differences of two variants during the study period, we estimate similar mean incubation periods (3.8 to 4.5 d) for both variants but a shorter mean generation interval for the Omicron variant (3.0 d; 95% CI: 2.7 to 3.2 d) than for the Delta variant (3.8 d; 95% CI: 3.7 to 4.0 d). The differences in estimated generation intervals may be driven by the “network effect”—higher effective transmissibility of the Omicron variant can cause faster susceptible depletion among contact networks, which in turn prevents late transmission (therefore shortening realized generation intervals). Using up-to-date generation-interval distributions is critical to accurately estimating the reproduction advantage of the Omicron variant. 

Inferring the relative strength (i.e. the ratio of reproduction numbers) and relative speed (i.e. the difference between growth rates) of new SARS-CoV-2 variants is critical to predicting and controlling the course of the current pandemic. Analyses of new variants have primarily focused on characterizing changes in the proportion of new variants, implicitly or explicitly assuming that the relative speed remains fixed over the course of an invasion. We use a generation-interval-based framework to challenge this assumption and illustrate how relative strength and speed change over time under two idealized interventions: a constant-strength intervention like idealized vaccination or social distancing, which reduces transmission rates by a constant proportion, and a constant-speed intervention like idealized contact tracing, which isolates infected individuals at a constant rate. In general, constant-strength interventions change the relative speed of a new variant, while constant-speed interventions change its relative strength. Differences in the generation-interval distributions between variants can exaggerate these changes and modify the effectiveness of interventions. Finally, neglecting differences in generation-interval distributions can bias estimates of relative strength. 

The COVID-19 pandemic has caused more than 1,000,000 reported deaths globally, of which more than 200,000 have been reported in the United States as of October 1, 2020. Public health interventions have had significant impacts in reducing transmission and in averting even more deaths. Nonetheless, in many jurisdictions, the decline of cases and fatalities after apparent epidemic peaks has not been rapid. Instead, the asymmetric decline in cases appears, in most cases, to be consistent with plateau- or shoulder-like phenomena—a qualitative observation reinforced by a symmetry analysis of US state-level fatality data. Here we explore a model of fatality-driven awareness in which individual protective measures increase with death rates. In this model, fast increases to the peak are often followed by plateaus, shoulders, and lag-driven oscillations. The asymmetric shape of model-predicted incidence and fatality curves is consistent with observations from many jurisdictions. Yet, in contrast to model predictions, we find that population-level mobility metrics usually increased from low levels before fatalities reached an initial peak. We show that incorporating fatigue and long-term behavior change can reconcile the apparent premature relaxation of mobility reductions and help understand when post-peak dynamics are likely to lead to a resurgence of cases. 

A novel coronavirus (SARS-CoV-2) emerged as a global threat in December 2019. As the epidemic progresses, disease modellers continue to focus on estimating the basic reproductive number R 0 —the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of R 0 during the beginning of the outbreak vary widely, despite relying on similar data sources. Here, we present a statistical framework for comparing and combining different estimates of R 0 across a wide range of models by decomposing the basic reproductive number into three key quantities: the exponential growth rate, the mean generation interval and the generation-interval dispersion. We apply our framework to early estimates of R 0 for the SARS-CoV-2 outbreak, showing that many R 0 estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of R 0 , including the shape of the generation-interval distribution, in efforts to estimate R 0 at the outset of an epidemic.