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 did not include two important taxa in our main analysis. The Influenza A virus genus was 159 excluded a posteriori because of a very weak phylogenetic signal for IT level ( Figure S9 ). On 160 inspection of the HA gene phylogeny it is apparent that although human infectivity and 161 transmissibility have evolved in only a few lineages (HA types) there is considerable variability 162 in IT level within those lineages, which would generate inflated counts of IT level change 163 ( Figure S10 ). Nonetheless, the phylogeny is broadly consistent with the pattern that most L3/4 164 lineages evolve from L1 lineages. We excluded Retroviridae from our main analysis a priori 165 because they cause chronic infections that allow far more time for within-host evolution prior 166 to transmission 9 . Consistent with this, we find that transmissible human lentiviruses (lineages 167 author/funder. All rights reserved. No reuse allowed without permission.