Fig. 3.

Simplot analysis to detect recombination and estimate breakpoint within the IBV/Mass/06 genome. (A) Relative gene location and similarity plot using IBV/Mass/06 as the query sequence. (B) Bootscan analysis showing multiple breakpoints designated as regions I–VIII. Complete genome nucleotide sequences used in the analysis were Cal = Cal99/NE15172/95, IBV/CK/CA99/99, CA/CA557/03, Conn = IBV/Conn/66, IBV/Conn/72, IBV/Conn/83, IBV/Conn/91, and Mass = IBV/Mass/65, IBV/Mass/72, IBV/Mass/79, IBV/Mass/85. The IBV/CK/A2 China strain was used in the analysis as an out-group. Both analyses were performed with the F84 distance model, window size of 1000 bp and step size of 40 bp.