Evolutionary origins of epidemic potential among human RNA viruses

Lu Lu; Liam Brierley; Gail Robertson; Feifei Zhang; Samantha Lycett; Donald Smith; Margo Chase-Topping; Peter Simmonds; Mark Woolhouse

We compiled a data pool of 7488 polymerase (or functional equivalent) gene sequences from The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/771394 doi: bioRxiv preprint biology 3 . However, we carried out a separate analysis for the one genus -Lentivirus -with 52 sufficient pol protein sequences available. Phylogenetic analysis 64 We performed parallel phylogenetic analyses using the BEAST software package 4 (V1.8.2). 65 We were primarily interested in tree topology; branch lengths scale to numbers of amino acid We tested the associations between IT levels and polymerase trees per genus using Phylogeny-74 trait association test (BaTS) 8 , inspecting both the Association index (AI) and Parsimony score 75 (PS) between genera. We observed that the Influenza A virus genus showed evidence of a 76 uniquely weak phylogenetic signal (Fig. S9a ) so this genus was subsequently considered 77 separately from the main analysis. Similar results were obtained using phylogenies based on 78 surface proteins as described below (Fig. S9b) . The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/771394 doi: bioRxiv preprint with an uncorrelated log-normal relaxed molecular clock model and with a constant size 86 coalescent process or Yule process prior over the phylogenies. Here, we allowed the branch 87 length to be scaled by substitution per site rather than by time (with ucld.mean equal to 1). The We applied asymmetric discrete trait models using BEAST to estimate IT level over each The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/771394 doi: bioRxiv preprint