Study design overview
Study design and data collection procedures for the Evaluating Modes of Influenza Transmission (EMIT) human challenge-transmission trial14 and the observational study of naturally infected influenza cases from University of Maryland campus community are described elsewhere (SI Appendix 1).15 Half-hour exhaled breath specimens are partitioned into fine (≤5µm) and coarse (>5µm) aerosol fractions during collection by Gesundheit-II bioaerosol sampler (G-II).16 Exhaled breath from both studies were evaluated using standard CDC qRT-PCR primers and probes at the University of Maryland laboratory. Nasopharyngeal swabs from experimental and natural cases were evaluated with the same reagents in separate labs. Nasopharyngeal swabs from the experimental group were not tested against a plasmid standard for experimental cases, limiting comparison of RNA shedding in swabs to the cycle threshold (Ct) values. Data were cleaned and analyzed in R (v3.5.1 R Development Core Team, Vienna, Austria) and SAS Studio (Release 3.7 (Enterprise Edition), v9.4M6, Cary, NC).