Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals.

"data availability primary data generated and analyzed in this study have been deposited in the sequence read archive (sra) under bioproject id: prjna758865. code for estimating transmission bottleneck sizes using the beta-binomial approach has been adapted from the original scripts available here: https://github com/koellelab/betabinomial_bottleneck (r version) h1n1 and h7n9 mean transmission bottleneck sizes were estimated using the approach outlined in a reanalysis study for sars-cov-2 deep sequencing data authored by . data availability primary data generated and analyzed in this study have been deposited in the sequence read archive (sra) under bioproject id: prjna758865"

"primer sequences are available in the github repository accompanying this manuscript ( ).; fastq files were processed using custom bioinformatic pipelines available on github https://github com/tcflab/sniffles2 .; code is available to replicate these analyses in the github repository accompanying this manuscript ( ).; code for estimating transmission bottleneck sizes using the beta-binomial approach has been adapted from the original scripts available here: https://github com/koellelab/betabinomial_bottleneck (r version) h1n1 and h7n9 mean transmission bottleneck sizes were estimated using the approach outlined in a reanalysis study for sars-cov-2 deep sequencing data authored by .; code to replicate these analyses is available in the github repository accompanying this manuscript ( )."

"Funding: This project was funded in part by National Institute of Allergy and Infectious Disease (NIAID) R01 AI125392—Mechanisms of influenza transmission bottlenecks: impact on viral evolution awarded to T.C.F. K.M.B. was supported by NIAID F30 (F30AI145182-02). L.A.H. was supported by the National Human Genome Research nstitute (NHGRI T32 (HG002760). The funders had no role in study design, data collection and analysis, the decision to publish, or the preparation of the manuscript."

"Funding This project was funded in part by National Institute of Allergy and Infectious Disease (NIAID) R01 AI125392—Mechanisms of influenza transmission bottlenecks: impact on viral evolution awarded to T.C.F. K.M.B. was supported by NIAID F30 (F30AI145182-02). L.A.H. was supported by the National Human Genome Research nstitute (NHGRI T32 (HG002760). The funders had no role in study design, data collection and analysis, the decision to publish, or the preparation of the manuscript."