skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants
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.  more » « less
Award ID(s):
1806833
PAR ID:
10461033
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Journal of The Royal Society Interface
Volume:
19
Issue:
191
ISSN:
1742-5662
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. In past work, time management interventions involving prompts, alerts, and planning tools have successfully nudged students in online courses, leading to higher engagement and improved performance. However, few studies have investigated the effectiveness of these interventions over time, understanding if the effectiveness maintains or changes based on dosage (i.e., how often an intervention is provided). In the current study, we conducted a randomized controlled trial to test if the effect of a time management intervention changes over repeated use. Students at an online computer science course were randomly assigned to receive interventions based on two schedules (i.e., high-dosage vs. low-dosage). We ran a two-way mixed ANOVA, comparing students' assignment start time and performance across several weeks. Unexpectedly, we did not find a significant main effect from the use of the intervention, nor was there an interaction effect between the use of the intervention and week of the course. 
    more » « less
  2. In this paper, we present a framework for quantifying the impact of interventions on the full trajectories of students' experiences. The interventions are given periodically based on student performance forecasting from an artificial intelligence (AI) model. We performed a small-scale randomized controlled trial for evaluating the impact of the AI-based intervention system on the undergraduate students of a science, technology, engineering, and mathematics (STEM) course. Intervention messaging content was based on machine learning forecasting models trained on data collected from the students in the same course over the preceding 3 years. Trial results show that the intervention produced a statistically significant increase in the proportion of students that achieved a passing grade. By applying the trajectory-analysis framework we find that the intervention impacts the stories of some types of students more than others, and use this to define new ways of identifying students who are most likely to benefit. Together these outcomes point to the potential and promise of just-in-time interventions for STEM learning and the need for larger fully-powered randomized controlled trials. 
    more » « less
  3. 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. 
    more » « less
  4. Carvalho, Paulo F. (Ed.)
    We present results from a small-scale randomized controlled trial that evaluates the impact of just-in-time interventions on the academic outcomes of N = 65 undergraduate students in a STEM course. Intervention messaging content was based on machine learning forecasting models of data collected from 537 students in the same course over the preceding 3 years. Trial results show that the intervention produced a statistically significant increase in the proportion of students that achieved a passing grade. The outcomes point to the potential and promise of just-in-time interventions for STEM learning and the need for larger fully-powered randomized controlled trials. 
    more » « less
  5. Abstract We developed a model to compare the impacts of different lifestyle interventions among prediabetes individuals and to identify the optimal age groups for such interventions. A stochastic simulation was developed to replicate the prediabetes and diabetes trends (1997–2010) in the U.S. adult population. We then simulated the population-wide impacts of three lifestyle diabetes prevention programs, i.e., the Diabetes Prevention Program (DPP), DPP-YMCA, and the Healthy Living Partnerships to Prevent Diabetes (HELP-PD), over a course of 10, 15 and 30 years. Our model replicated the temporal trends of diabetes in the U.S. adult population. Compared to no intervention, the diabetes incidence declined 0.3 per 1,000 by DPP, 0.2 by DPP-YMCA, and 0.4 by HELP-PD over the 15-year period. Our simulations identified HELP-PD as the most cost-effective intervention, which achieved the highest 10-year savings of $38 billion for those aged 25–65, assuming all eligible individuals participate in the intervention and considering intervention achievement rates. Our model simulates the diabetes trends in the U.S. population based on individual-level longitudinal data. However, it may be used to identify the optimal intervention for different subgroups in defined populations. 
    more » « less