Fig. 5: Population diversity is reduced when the influenza virus moves from the upper to the lower respiratory tract in ferrets.
a Ferrets were inoculated with a site-specific intranasal dose of 105 PFU of dual-barcoded A/CA/07/2009 HA-K153E PASTN virus containing the NheI registration mark. Ferret weight was monitored daily. b Viral titer in ferret nasal washes were determined by TCIDGlo50. c Changes in frequency for HA (top) and PA (bottom) barcodes present in nasal wash samples over the course of infection. d Evenness, Shannon’s diversity index, and Gini-Simpson index for the indicated viral populations. e The richness of each tissue is indicated by the number of distinct barcodes in each sample. N.A. = not attempted. f Virus was recovered from the trachea at 5 dpi and the frequency of barcodes was determined. Distinct dominant barcodes are identified by colored asterisks. g HA barcode frequencies were compared between the nasal wash (3 dpi) and trachea (5 dpi) for ferret 34, 35, and 36. Red arrowheads highlight dominant barcodes with frequency > 30%. R = Pearson’s correlation coefficient. Note that barcodes unique to the nasal wash or trachea are not plotted here. h Virus was recovered from lung lobes 5 dpi and the frequency of barcodes was determined. Lung lobes: upper left (UL), lower left (LL), upper right (UR), middle right (MR), lower right (LR). Distinct dominant barcodes are identified by colored asterisks, matching those in g where appropriate. The limit of detection for viral titer assays is indicated by a dashed line in b. Source data are provided as a Source Data file.
