Figure 4.

Scientific Use Case Comparing Human and Civet SARS-CoV Isolates. The results that were obtained from the various analytical and visualization tools provided in ViPR and explored in the scientific use case are shown. (a) A portion of a multiple sequence alignment of strains isolated from 2003 through 2004, from either humans (white labels) or civets (gray labels), including a column found to significantly differ between the specified groups based on meta-CATS analysis. (b) A Maximum Likelihood phylogenetic tree color-coded by host of isolation. Horizontal branch lengths are proportional to distance (the proportion of nucleotide changes). The distance scale for the proportion of changes is provided at the bottom of the panel. Strains belonging to the “civet-predominate” (CP) or “human-predominate” (HP) clades are delineated with blue braces. (c) An abridged table of the meta-CATS output containing significant positions, raw chi-square values, C-values (roughly equivalent to p-values), chi-square degrees of freedom and residue diversity for a subset of significant positions identified across the genome. (d) A 3D homodimeric protein structure of the SARS-CoV Spike protein showing secondary structure in cartoon and positions 479 and 487 (highlighted in blue on one of the monomeric chains), which were identified as significantly differing between hosts at the nucleotide level by meta-CATS.