Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2
Proceedings of the National Academy of Sciences, vol. 120, pp. e2221887120
Abstract
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.
Authors 12
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Affiliation as printed
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
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National Institutes of Health · Fogarty International Center
Affiliation as printed
Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
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London School of Hygiene & Tropical Medicine
Affiliation as printed
Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
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Affiliation as printed
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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Affiliation as printed
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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Georgia Institute of Technology · Institut de Biologie de l'École Normale Supérieure
Affiliation as printed
Institut de Biologie, École Normale Supérieure, Paris 75005, France
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
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London School of Hygiene & Tropical Medicine
Affiliation as printed
Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
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Affiliation as printed
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08542
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08542
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National Institute for Public Health and the Environment
Affiliation as printed
Center for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 Bilthoven, The Netherlands
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Leiden University Medical Center · National Institute for Public Health and the Environment
Affiliation as printed
Center for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 Bilthoven, The Netherlands
Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 Leiden, The Netherlands
Center for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 Bilthoven, The Netherlands; Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 Leiden, The Netherlands
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National Institutes of Health · Fogarty International Center
Affiliation as printed
Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
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Affiliation as printed
Department of Biology, McMaster University, Hamilton, L8S 4L8 ON, Canada
Department of Mathematics and Statistics, McMaster University, Hamilton, L8S 4L8 ON, Canada
M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8S 4L8 ON, Canada
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