MERS-CoV spillover at the camel-human interface

Gytis Dudas; Luiz Max Carvalho; Andrew Rambaut; Trevor Bedford; Ali M. Somily; Mazin Barry; Sarah S. Al Subaie; Abdulaziz A. BinSaeed; Fahad A. Alzamil; Waleed Zaher; Theeb Al Qahtani; Khaldoon Al Jerian; Scott J.N. McNabb; Imad A. Al-Jahdali; Ahmed M. Alotaibi; Nahid A. Batarfi; Matthew Cotten; Simon J. Watson; Spela Binter; Paul Kellam

. CC-BY-NC 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/173211 doi: bioRxiv preprint Figure S10 . Tests of recombination across MERS-CoV clades. Maximum clade credibility tree of MERS-CoV genomes annotated with results of two recombination detection tests (PHI and 3Seq) applied to descendent sequences of each clade. Both tests identify large portions of existing sequence data as containing signals of recombination. Note that markings do not indicate where recombinations have occurred on the tree, merely the minimum distance in sequence/time space between recombining lineages. Figure S11 . MERS-CoV genomes exhibit high numbers of non-clonal loci. Ancestral state reconstruction (right) identifies a large number of sites in which mutations have occurred more than once in the tree (homoplasies, orange) or are reversions (red) from a state arising in an ancestor. Mutations that apparently only occur once in the tree (synapomorphies) are shown in grey. The maximum likelihood phylogeny on the left is coloured by whether sequences were sampled in humans (blue) or camels (orange). Figure S12 . Human clade sharing between genomic fragments 1 and 2. Central scatter plot shows the posterior probability of human clades shared between genomic fragments 1 and 2, in their respective trees. Left and bottom scatter plots track the posterior probability of human clades only observed in fragment 2 (left) or fragment 1 (bottom). The cumulative probability of human clades present in either tree are tracked by plots on the right (fragment 2) and top (fragment 1). Most of the probability mass is concentrated within human clades that are present in trees of both genomic fragment 1 and 2 (0.9701 and 0.9474 of all human clades across posteriors, respectively).