Infectious Disease
Estimating the generation time for influenza transmission using household data in the United States Louis Yat Hin Chan* Louis Yat Hin Chan Sinead E. Morris Melissa S. Stockwell Natalie M. Bowman Edwin Asturias Suchitra Rao Karen Lutrick Katherine Ellingson Huong Q. Mclean Edward A. Belongia Yvonne Maldonado Jessica E. Biddle Sarah E. Smith-Jeffcoat Matthew Biggerstaff Melissa Rolfes H. Keipp Talbot Carlos G. Grijalva Rebecca K. Borchering Alexandra M. Mellis
The generation time (GT), representing the interval between infections in primary and secondary cases, is essential for understanding and predicting the transmission dynamics of seasonal influenza, including the effective reproduction number (Rt). However, comprehensive GT estimates for seasonal influenza, especially post-2009, are lacking. As a substitute, the serial interval, defined as the duration between symptom onsets of successive cases, is often used due to the practicality of observing symptom onsets.
We estimated the GT utilizing data from a 7-site case-ascertained household study in the United States over 2 influenza seasons, 2021-22 and 2022-23. Over 200 individuals with influenza and their household contacts were enrolled within 7 days of the first illness in the household, and prospectively followed for 10 days of daily symptom monitoring and nasal swab collection. Households with more than one primary case, defined by date of first symptom onset in the household, were excluded. Influenza was detected through polymerase chain reaction (PCR) testing of nasal swabs collected daily from exposed household contacts. 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) GT. We also assessed estimate sensitivity by varying the incubation period.
We estimated a mean intrinsic GT of approximately 3.0 (95% credible interval, CI: 2.7-3.2) days, with the realized household GT marginally shorter with an estimate of 2.6 (95% CI: 2.4-2.8) days. The GT exhibited limited sensitivity to the incubation period.
Our study contributes to the ongoing efforts to refine estimates of the GT for influenza. Our estimates, derived from the recent data, fall within the uncertainty bounds of previous estimates, suggesting consistency, and will be incorporated into real-time Rt estimation efforts.
