Estimating the generation time for SARS-CoV-2 transmission using United States household data, December 2021–May 2023
Generation time, representing the interval between infection events in primary and secondary cases, is important for understanding disease transmission dynamics including predicting the effective reproduction number (Rt), which informs public health decisions. While previous estimates of SARS-CoV-2 generation times have been reported for early Omicron variants, there is a lack of data for subsequent sub-variants, such as XBB. We estimated SARS-CoV-2 generation times using data from the Respiratory Virus Transmission Network – Sentinel (RVTN-S) household transmission study conducted across seven U.S. sites from December 2021 to May 2023. The study spanned three Omicron sub-periods dominated by the sub-variants BA.1/2, BA.4/5, and XBB. We employed a Susceptible-Exposed-Infectious-Recovered (SEIR) model with a Bayesian data augmentation method that imputes unobserved infection times of cases to estimate the generation time. The estimated mean generation time for the overall Omicron period was 3.5 days (95% credible interval, CrI: 3.3–3.7). During the sub-periods, the estimated mean generation times were 3.8 days (95% CrI: 3.4–4.2) for BA.1/2, 3.5 days (95% CrI: 3.3–3.8) for BA.4/5, and 3.5 days (95% CrI: 3.1–3.9) for XBB. Our study provides estimates of generation times for the Omicron variant, including the sub-variants BA.1/2, BA.4/5, and XBB. These up-to-date estimates specifically address the gap in knowledge regarding these sub-variants and are consistent with earlier studies. They enhance our understanding of SARS-CoV-2 transmission dynamics by aiding in the prediction of Rt, offering insights for improving COVID-19 modeling and public health strategies.
Authors
- Yvonne Maldonado (ORCID: https://orcid.org/0000-0002-5664-5583)
- Quenla Haehnel
- Rosita Thiessen
- Miriana Moreno Zivanovich (ORCID: https://orcid.org/0000-0002-3930-1551)
- Lisa Saiman (ORCID: https://orcid.org/0000-0002-7231-8451)
- Yuan J Carrington (ORCID: https://orcid.org/0000-0003-1615-5587)
- Frank Zhou
- Suryakala Sarilla
- Elisha Stefanski
- Edwin J. Asturias (ORCID: https://orcid.org/0000-0002-1275-0787)
- Erica Joan Pruett Anderson
- Rasika Behl (ORCID: https://orcid.org/0000-0002-5942-3564)
- Leanne X Chun (ORCID: https://orcid.org/0000-0002-4304-4017)
- Onika Abrams
- Ferris Alaa Ramadan
- Jennifer K. Meece (ORCID: https://orcid.org/0000-0002-6486-3505)
- Alexandra M. Mellis (ORCID: https://orcid.org/0000-0001-6756-1425)
- Paige Yates
- Edward A. Belongia (ORCID: https://orcid.org/0000-0001-7478-0415)
- Natalie M. Bowman (ORCID: https://orcid.org/0000-0003-4260-8009)
- Matthew Biggerstaff (ORCID: https://orcid.org/0000-0001-5108-8311)
- Andrea Stafford Hintz
- Sinead E. Morris (ORCID: https://orcid.org/0000-0001-8626-1698)
- Emma Stainton (ORCID: https://orcid.org/0000-0002-4247-8059)
- Jorge E Celedonio
- Son H. McLaren (ORCID: https://orcid.org/0000-0001-9947-588X)
- Louis Yat Hin Chan (ORCID: https://orcid.org/0000-0002-4689-6995)
- Leila Deering
- Kathleen Grice
- Rebecca K. Borchering (ORCID: https://orcid.org/0000-0003-4309-2913)
- Grace K-Y. Tam (ORCID: https://orcid.org/0000-0001-5308-1439)
- Raul A. Silverio Francisco
- Carla Rottscheit
- Katherine Ellingson (ORCID: https://orcid.org/0000-0001-7624-312X)
- Jonathan Altamirano (ORCID: https://orcid.org/0000-0002-0968-3333)
- Mokenge Ndiva Mongoh
- Dayton D. Marchlewski
- Sandy Strey
- Daniel Chandler (ORCID: https://orcid.org/0000-0002-9413-8443)
- Ayla Bullock
- Brianna Schibley-Laird
- Judy A. King
- Ine Sohn
- Chris Lindsell
- Huong Q. Nguyen
- Melissa S. Stockwell
- Josue Ortiz
- Flavia Maria Nakayima Miiro
- Miriah Rotar
- Melissa A. Rolfes
- Jackson Resser
- Hsi-nien Jubilee Tan
- Sonia Chavez
- Maria Catalina Padilla-Azain
- Sarah E. Smith-Jeffcoat
- Samantha A. Ferguson
- Ryan Dalforno
- Cameron Bendalin
- Alexis Perry
- Melody Liu
- Ana M. Valdez de Romero
- H. Keipp Talbot
- Amelia Dodds
- Samuel Massion
- Carrie Marcis
- Afan Swan
- Katherine Katie Murray
- Ruby Swaimn
- Jessica E. Biddle
- Mason Speirs
- Gina Burbey
- Timothy Williams
- Julienne Reynolds
- Carlos G. Grijalva
- Brittney Figueroa
- Brianna Freund
- Amy Yang
- Jessica Lin
- Suchitra Rao
- Ellen Sano
- Anna McShea
- Alondra A. Aguilar
- Lauren Milner
- Vicki Moon
- Cara Lwin
- Karen Lutrick
- Jennifer Moran
- Brittany Creasman
- Joshua Petrie
- DeeAnn Hertel
- Anny L.Diaz Perez
- Garrett Heuer
- Hannah Berger
- Sarah Kopitzke
- Melissa Strupp
- Marcela Lopez
- The RVTN-Sentinel Study Group
- Jolie Granger
- John Meghreblian
Institutions
- University of North Carolina at Chapel Hill (US)
- Centers for Disease Control and Prevention (US)
- Marshfield Clinic (US)
- University of Arizona (US)
- Columbia University Irving Medical Center (US)
- Children's Hospital Colorado (US)
- Vanderbilt University Medical Center (US)
- University of Colorado Denver (US)
- Stanford University (US)
Publication Details
- Journal
- Scientific Reports
- Published
- 2026-04-11
- DOI
- https://doi.org/10.1038/s41598-026-46596-6
- Primary Topic
- COVID-19 epidemiological studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institutes of Health
- Centers for Disease Control and Prevention