Figure 1.
DNA maximum-likelihood trees of the HA segment.
illustrating relationships between IAV hemagglutinin subtypes. Branch lengths represent the number of nucleotide substitutions between close HA subtypes (scale bars represent 10% of nucleotide substitutions). Adapted from Fouchier et al. 2005.
Figure 2.
Examples of consecutive IAV infections in seven individuals.
The subtypes of detected viruses, as well as time between detections, are given.
Figure 3.
Contingency table for HA re-infections with the IAV subtypes most frequently isolated.
Rows represent the HA subtype in the first detected infection and columns the HA from an infection retrieved ≥7 days later. The number in each box represents the number of cases, together with standardized Pearson's residuals in brackets. Red boxes show negative values and represent a deficiency of cases, blue boxes show positive values and an overrepresentation of cases, and grey denote cases that do not depart from expected values. The dendrogram on top illustrates HA subtype phylogenetic relatedness.
Table 1.
Contingency table for HA re-infections with common HA clades.
Table 2.
Contingency table for HA re-infections with HA groups.
Figure 4.
IAV detection probability for H1 and H3 Clades as a function of time and previously detected infections.
The x-axis represents time in days since first detection of a virus. The y-axis depicts the probability of detection. Black continuous line represents the change over time in probability (95% CI with dashed lines). The horizontal blue line is the probability of detection of an infection with a virus from a specific clade for naïve birds (95% CI with dashed lines). The distribution of data points is presented as rug plots along the x-axis. Detection probabilities for H1 (A) and H3 (C) Clades for individuals that have previously experienced an infection with a virus from the same clade. Detection probabilities for H1 (B) and H3 (D) Clades for individuals that have previously experienced an infection with a virus from another clade.
Table 3.
Contingency table for NA re-infections.