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 recognise that there will be significant gaps in our knowledge of mammal/bird non-RT 143 RNA virus diversity: new species are routinely being identified 8 and virus genome sequences 144 are accumulating rapidly ( Figure S1 ). Our selection procedure resulted in a data set with only 145 28% of virus sequences from human hosts, but it is still likely that the phylogenetic diversity 146 of viruses from non-human hosts is greatly underestimated relative to that from humans 3,14 , 147 noting that for many mammal/bird taxa no RNA viruses at all have yet been reported. There 148 will also be gaps in our knowledge of IT level: some viruses originally classified as L1 have 149 been subsequently found to human infective; and some viruses originally classified as L2 have 150 been subsequently found to be human transmissible as epidemiological data accumulates 6 . As 151 new virus sequences are added and IT levels are assigned or (occasionally) re-assigned it is 152 entirely possible that the estimated ancestors of some L3/4 viruses will change. However, we 153 anticipate that the impact of such changes across the whole data set will be to strengthen our 154 main conclusions. This is because we anticipate that far more L1 viruses will be added than 155 L2, and more L2 than L3/4, continuing the current trend ( Figure S1 ). For this reason, we 156 consider our estimate that 74% of L3/4 viruses arose from L1 lineages to be conservative.