Fig. 2: Performance of environmental samples (ES) is dependent on poultry host species and sample type.
A Principal coordinate analysis (PCoA) of beta-diversity (Jaccard) of poultry virus species. PERMANOVA was calculated adjusting for both location and time as a confounder. The eigen values are reported showing the variation reported by PCo1 and PCo2. B Based on the PCoA in A, we calculated the median centroid of each group by determining the median PCo1 and PCo2 coordinates. Relative to poultry swabs, we calculated the distance of all samples from (C) chicken oropharyngeal (n = 15), (D) chicken cloacal (n = 15), (E) duck oropharyngeal (n = 14), and (F) duck cloacal (n = 15) median centroids, as shown in panel B. Comparative environmental samples were collected from air (holding area, n = 13; slaughter area, n = 14; outside, n = 10), wash water (n = 19) drinking water (n = 9), and cage swabs (n = 17). Each group is ranked from the shortest to longest distance from its respective poultry median centroid. Spearman correlations between virus abundance in reads per million (RPM) and the distance from (G) chicken oropharyngeal, H chicken cloacal (P value shown = 0.0003), I duck oropharyngeal (P value shown = 0.0001), and (J) duck cloacal (P value shown = 0.0001) median centroids were calculated for viruses either recaptured (n = 45) or undetected (n = 38) by environmental sampling, as shown in Fig. 1A. Each point represents an individual virus species, and therefore n values correspond to the number of distinct viruses rather than biological replicates. Boxplots display the median (centre line), interquartile range (box), and whiskers extending to 1.5× the interquartile range; points represent individual samples. K Ridge plot showing the probability of each poultry swab being the source of pathogenic viruses for all environmental samples. Statistics were calculated using a Kruskal-Wallis with Dunns post-hoc test. All P values obtained were corrected for false-discovery rate (FDR) using the Benjamini-Hochberg method. P values are annotated as follows: P < 0.05 *; P < 0.01 **; P < 0.001***.
