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).