Figure 2

Patterns of infection in experimental Mallards. A, C, E Refer to cloacal drinking experiments, B, D, F refer to the preening experiments. A, B Virus shedding, represented by Cq values on an inverted Y-axis, where a low Cq value is indicative of high levels of shedding. For each trial, box and whiskers plots are shown for each day of the experiment which illustrate the median (black line) and spread of the data (upper and lower quartiles). Different colours correspond to different days. C, D Proportion of individuals with positive staining for IAV in each tissue across the gastrointestinal tract. The X axis is divided into experimental trial, and within trials subdivided into tissue from different parts of the gastrointestinal tract, J1 to B, ranging from light blue to dark blue. E, F Heatmap of intensity of infection as inferred by relative number of positive cells for each individual and tissue. Values range from 0 (no positive staining), 0.5 (positive cells present), 1 (mild), 2 (moderate), to 3 (marked staining). Each individual for each experiment is plotted along the Y axis (R, B, G, Y, W), and tissue type across the X axis. For C–F, tissues assessed are two sections of jejunum J1, J2, two sections of ileum I3, I4, colon C, and bursa B. An asterisk indicates no bursal tissue could be identified. In the final cloacal drinking trial, only four ducks were included, where all other experiments have n = 5. Intensity scores and Cq values for individual ducks are presented in Additional file 2.