Our understanding of influenza transmission remains imperfect due to the high prevalence of asymptomatic infections that often go undetected. To address this challenge, we leveraged uniquely resolved data from a household cohort study spanning three consecutive years in rural and urban South Africa. The study incorporated pre-season serum collection and twice-weekly virological testing during the influenza season, regardless of symptom presence. We developed a subtype/lineage-specific influenza household transmission model that accounts for time-resolved viral shedding across the full clinical spectrum of infections, allowing us to disentangle the role of household and community exposures, pre-season immunity, and age on transmission. Our analysis revealed that viral shedding intensity, as measured by the cycle threshold (Ct) values of infected household members, significantly correlated with the risk of transmission for all four influenza subtypes/lineages. After adjusting for viral shedding, pre-season hemagglutination inhibition (HAI) titers greater than 1:40 were associated with a significantly lower risk of infection acquisition for A(H1N1)pdm09, A(H3N2), and B/Victoria, but not for B/Yamagata. Notably, children exhibited higher susceptibility, longer viral shedding durations, and higher peak viral loads compared to adults across all subtypes/lineages, even after adjusting for pre-season HAI titers. While our findings support that HAI titers correlate with protection, the strong residual effects of age on susceptibility and viral shedding may reflect the accumulation of additional immune responses shaped by repeated exposures over time. Our study underscores the need to explore immune mechanisms beyond HAI titers that modulate influenza susceptibility and transmission.

CC has received grant support from Sanofi Pasteur, US CDC, the Bill & Melinda Gates Foundation, the Taskforce for Global Health, Wellcome Trust and the South African Medical Research Council. AvG has received grant support from Sanofi Pasteur, Pfizer related to pneumococcal vaccine, CDC and the Bill & Melinda Gates Foundation. NW reports grants from Sanofi Pasteur and the Bill & Melinda Gates Foundation. NAM has received a grant to his institution from Pfizer to conduct research in patients with pneumonia and from Roche to collect specimens to assess a novel TB assay.

Data collection of the PHIRST flu study was supported by the National Institute for Communicable Diseases of the National Health Laboratory Service and the US Centers for Disease Control and Prevention (cooperative agreement number 5U51IP000155). Molly Sauter would like to acknowledge support from Princeton University Office of Undergraduate Research Undergraduate Fund for Academic Conferences through the President’s Fund. Bryan Grenfell would like to acknowledge support from Princeton Catalysis and Princeton Precision Health.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The PHIRST protocol was approved by the University of the Witwatersrand Human Research Ethics Committee (Reference 150808) and the US CDC's Institutional Review Board relied on the local review (#6840). The protocol was registered on http://clinicaltrials.gov on 6 August 2015 (Reference NCT02519803). Participants provided individual written consent or assent prior to enrollment and received a grocery store voucher of ZAR25–30 (USD 2–2.5) per visit for their time. (See 45 C.F.R. part 46.114; 21 C.F.R. part 56.114).

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

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I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

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I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

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The study protocol including informed consent forms is available on the NICD website (https://www.nicd.ac.za/wp-content/uploads/2021/02/PHIRST-SARS-CoV-2-protocol-V1-amendment-Nov2020-incl-upd-consent.pdf). The investigators welcome enquiries about possible collaborations and requests for access to the data set. Data will be shared after approval of a proposal and with a signed data access agreement. Investigators interested in more details about this study, or in accessing these resources, should contact the principle investigator, Prof Cheryl Cohen, at NICD (cherylcnicd.ac.za).