FIG. 4.

Bootscan analysis of the S gene to detect recombination. Bootscanning was conducted with Simplot on a gapless nucleotide alignment, generated with ClustalX, with the SARS S gene as the query sequence. The dashed line denotes the feline infectious peritonitis virus (X06170), while the solid line denotes the avian infectious bronchitis virus (M95169). The greater the percentage of permuted trees, the greater the sequence identity to the SARS S sequence. Other taxa that were included in the alignment but had less than 10% permuted trees were murine hepatitis virus (AF208066) and human coronavirus OC43 (L14643).