R code used to perform statistical analyses and create figures as part of this research study and manuscript on the comparative evaluation of airborne influenza virus shedding in ferrets.
Source_Data directory contains the source data used to make manuscript Figure 1, created in GraphPad Prisim v10.5.0, as well as for supplemental figures 1 and 2 (Figures_1_S1_S2_source_data.xlsx), along with a PNG file for import and use with figpatch in R (Figure_5C_table-heatmap.png), and all other source data for analysis and figure creation in R (FullData.csv).
AR_analysis.R script is self contained. Requires the relevent R packages installed, found in the script and in the section below. Whole script should only take a few minutes to run. However, output commands such as figure outputs using ragg has been commented out to make the output of figure files optional.
Pulit-Penaloza JA, Kieran TJ, Brock N, Belser JA, Sun X, Zeng H, Pappas C, De La Cruz JA, Hatta Y, Di H, Davis TC, Tumpey TM, Maines TR. (2026). Advancing A(H5N1) influenza risk assessment in ferrets through comparative evaluation of airborne virus shedding patterns. Nature Communications. 17, 2266. https://doi.org/10.1038/s41467-026-68931-1
Recent A(H5N1) zoonotic cases linked to poultry and cattle in North America highlight the urgent need to assess the pandemic potential of emerging strains. Using male ferrets, we evaluate two B3.13 and two D1.1 genotype A(H5N1) viruses isolated from humans and observe fatal disease and varying capacities for direct contact transmission. To enhance pandemic risk assessment, we conduct aerosol sampling using cyclone BC251 and water condensation capture-based SPOT samplers and perform comparative analyses to include additional A(H5N1), A(H9N2), A(H7N9), and A(H1N1)pdm09 strains with known transmissibility profiles. Although none of the A(H5N1) strains transmit via the air, B3.13 viruses are detected at significantly higher levels compared to D1.1 strains. Here we show strong correlations between viral loads in nasal washes, airborne virus shedding, and transmissibility in ferrets, highlighting the value of these metrics for identifying zoonotic influenza viruses that may be adapting toward increased transmission potential.
R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 26100)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.3.0 tidylog_1.1.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[6] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[11] ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.5 compiler_4.4.0 Rcpp_1.0.13 tidyselect_1.2.1
[5] magick_2.8.5 scales_1.3.0 figpatch_0.3.0 R6_2.5.1
[9] generics_0.1.3 munsell_0.5.1 pillar_1.10.2 tzdb_0.4.0
[13] rlang_1.1.4 stringi_1.8.4 timechange_0.3.0 cli_3.6.3
[17] withr_3.0.1 magrittr_2.0.3 grid_4.4.0 rstudioapi_0.16.0
[21] hms_1.1.3 clisymbols_1.2.0 lifecycle_1.0.4 vctrs_0.6.5
[25] glue_1.8.0 farver_2.1.2 colorspace_2.1-1 tools_4.4.0
[29] pkgconfig_2.0.3
Other: ragg_1.3.3 rstatix_0.7.2 figpatch_0.3.0
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