
==== Front
medRxiv
MEDRXIV
medRxiv
Cold Spring Harbor Laboratory

10.1101/2024.08.17.24312064
preprint
1
Article
Estimating the generation time for influenza transmission using household data in the United States
Chan Louis Yat Hin http://orcid.org/0000-0002-4689-6995

Morris Sinead E. http://orcid.org/0000-0001-8626-1698

Stockwell Melissa S. http://orcid.org/0000-0002-2113-7247

Bowman Natalie M. http://orcid.org/0000-0003-4260-8009

Asturias Edwin http://orcid.org/0000-0002-1275-0787

Rao Suchitra http://orcid.org/0000-0002-0334-6301

Lutrick Karen http://orcid.org/0000-0003-3480-849X

Ellingson Katherine D. http://orcid.org/0000-0001-7624-312X

Nguyen Huong Q. http://orcid.org/0000-0003-2725-6439

Maldonado Yvonne http://orcid.org/0000-0002-5664-5583

McLaren Son H. http://orcid.org/0000-0001-9947-588X

Sano Ellen http://orcid.org/0000-0002-2202-448X

Biddle Jessica E. http://orcid.org/0000-0002-3161-7121

Smith-Jeffcoat Sarah E. http://orcid.org/0000-0002-7962-9017

Biggerstaff Matthew http://orcid.org/0000-0001-5108-8311

Rolfes Melissa A. http://orcid.org/0000-0002-0483-9941

Talbot H. Keipp http://orcid.org/0000-0003-0141-1760

Grijalva Carlos G. http://orcid.org/0000-0002-2329-7797

Borchering Rebecca K. http://orcid.org/0000-0003-4309-2913

Mellis Alexandra M. http://orcid.org/0000-0001-6756-1425

RVTN-Sentinel Study Group
19 8 2024
2024.08.17.24312064https://creativecommons.org/publicdomain/zero/1.0/ To the extent possible under law, the person who associated CC0 with this work has waived all copyright and related or neighboring rights to this work.
http://medrxiv.org/lookup/doi/10.1101/2024.08.17.24312064
nihpp-2024.08.17.24312064.pdf
The generation time, representing the interval between infections in primary and secondary cases, is essential for understanding and predicting the transmission dynamics of seasonal influenza, including the real-time effective reproduction number (Rt). However, comprehensive generation time estimates for seasonal influenza, especially post the 2009 influenza pandemic, are lacking. We estimated the generation time utilizing data from a 7-site case-ascertained household study in the United States over two influenza seasons, 2021/2022 and 2022/2023. More than 200 individuals who tested positive for influenza and their household contacts were enrolled within 7 days of the first illness in the household. All participants were prospectively followed for 10 days completing daily symptom diaries and collecting nasal swabs, which were tested for influenza via RT-PCR. We analyzed these data by modifying a previously published Bayesian data augmentation approach that imputes infection times of cases to obtain both intrinsic (assuming no susceptible depletion) and realized (observed within household) generation times. We assessed the robustness of the generation time estimate by varying the incubation period, and generated estimates of the proportion of transmission before symptomatic onset, infectious period, and latent period. We estimated a mean intrinsic generation time of 3.2 (95% credible interval, CrI: 2.9-3.6) days, with a realized household generation time of 2.8 (95% CrI: 2.7-3.0) days. The generation time exhibited limited sensitivity to incubation period variation. Estimates of the proportion of transmission that occurred before symptom onset, the infectious period, and the latent period were sensitive to variation in incubation periods. Our study contributes to the ongoing efforts to refine estimates of the generation time for influenza. Our estimates, derived from recent data following the COVID-19 pandemic, are consistent with previous pre-pandemic estimates, and will be incorporated into real-time Rt estimation efforts.
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pmc
