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

In contrast to IT levels, host categories are not mutually exclusive traits of a virus 123 species/subtype, and for some genera (e.g. Ebolavirus) it is likely that we are missing sequences 124 from the reservoir host(s). Therefore, we did not attempt a discrete traits analysis for host range 125 but compared the known non-human hosts for L2 and L3/4 viruses at the species/subtype and 126 genus levels (see Supplementary Materials). At the species/subtype level human viruses also 127 found in non-human primates were most likely to be L3/4 rather than L2; those also found in 128 birds were least likely (Figure 4) . At the genus level the pattern was similar (Spearman's rank 129 correlation of coefficient estimates by host category = +0.89, P<0.01) but the confidence In keeping with earlier work 15 , we used RNA-dependent RNA polymerase protein-based 136 phylogenies in our main analysis. However, we tested the possibility that alternative 137 phylogenies would generate different numbers and distributions of transitions between traits 138 by constructing alternatives trees based on surface protein sequences ( Figure S8 ). We obtained 139 results that differed minimally from our main analysis, most importantly that an estimated 71% 140 of L3/4 lineages have L1 ancestors (see Data File 9) .